diff --git a/docs/404.html b/docs/404.html
index 24e70f1..eae9d9d 100644
--- a/docs/404.html
+++ b/docs/404.html
@@ -24,7 +24,7 @@
     
     <a class="navbar-brand me-2" href="https://gdrplatform.github.io/gDRimport/index.html">gDRimport</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/PULL_REQUEST_TEMPLATE.html b/docs/PULL_REQUEST_TEMPLATE.html
index 4faa6c6..991ccf6 100644
--- a/docs/PULL_REQUEST_TEMPLATE.html
+++ b/docs/PULL_REQUEST_TEMPLATE.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="index.html">gDRimport</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/articles/ConvertingMAEtoPharmacoSet.html b/docs/articles/ConvertingMAEtoPharmacoSet.html
index 1b47256..96c51b9 100644
--- a/docs/articles/ConvertingMAEtoPharmacoSet.html
+++ b/docs/articles/ConvertingMAEtoPharmacoSet.html
@@ -26,7 +26,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">gDRimport</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -165,7 +165,7 @@ <h2 id="converting-the-mae-object-into-a-pharmacoset-object">Converting the MAE
 <code class="sourceCode R"><span><span class="va">pset</span></span>
 <span><span class="co">#&gt; &lt;PharmacoSet&gt;</span></span>
 <span><span class="co">#&gt; Name:  Kyung2022 </span></span>
-<span><span class="co">#&gt; Date Created:  Thu Nov  7 10:37:05 2024 </span></span>
+<span><span class="co">#&gt; Date Created:  Mon Dec  9 10:53:32 2024 </span></span>
 <span><span class="co">#&gt; Number of samples:  7 </span></span>
 <span><span class="co">#&gt; Molecular profiles:</span></span>
 <span><span class="co">#&gt;    A MultiAssayExperiment object of 1 listed</span></span>
@@ -1282,7 +1282,7 @@ <h2 id="references">References<a class="anchor" aria-label="anchor" href="#refer
 <span><span class="co">#&gt; [8] base     </span></span>
 <span><span class="co">#&gt; </span></span>
 <span><span class="co">#&gt; other attached packages:</span></span>
-<span><span class="co">#&gt;  [1] MultiAssayExperiment_1.28.0 gDRimport_1.5.2            </span></span>
+<span><span class="co">#&gt;  [1] MultiAssayExperiment_1.28.0 gDRimport_1.5.3            </span></span>
 <span><span class="co">#&gt;  [3] PharmacoGx_3.6.0            CoreGx_2.6.1               </span></span>
 <span><span class="co">#&gt;  [5] SummarizedExperiment_1.32.0 Biobase_2.62.0             </span></span>
 <span><span class="co">#&gt;  [7] GenomicRanges_1.54.1        GenomeInfoDb_1.38.8        </span></span>
@@ -1293,21 +1293,21 @@ <h2 id="references">References<a class="anchor" aria-label="anchor" href="#refer
 <span><span class="co">#&gt; loaded via a namespace (and not attached):</span></span>
 <span><span class="co">#&gt;   [1] bitops_1.0-9            rlang_1.1.4             magrittr_2.0.3         </span></span>
 <span><span class="co">#&gt;   [4] shinydashboard_0.7.2    compiler_4.3.0          reshape2_1.4.4         </span></span>
-<span><span class="co">#&gt;   [7] maps_3.4.2              systemfonts_1.0.5       vctrs_0.6.5            </span></span>
-<span><span class="co">#&gt;  [10] relations_0.6-13        stringr_1.5.1           pkgconfig_2.0.3        </span></span>
+<span><span class="co">#&gt;   [7] maps_3.4.2.1            systemfonts_1.0.5       vctrs_0.6.5            </span></span>
+<span><span class="co">#&gt;  [10] relations_0.6-14        stringr_1.5.1           pkgconfig_2.0.3        </span></span>
 <span><span class="co">#&gt;  [13] crayon_1.5.3            fastmap_1.2.0           backports_1.5.0        </span></span>
 <span><span class="co">#&gt;  [16] XVector_0.42.0          caTools_1.18.3          utf8_1.2.4             </span></span>
-<span><span class="co">#&gt;  [19] promises_1.3.0          rmarkdown_2.29          pracma_2.4.4           </span></span>
+<span><span class="co">#&gt;  [19] promises_1.3.2          rmarkdown_2.29          pracma_2.4.4           </span></span>
 <span><span class="co">#&gt;  [22] ragg_1.2.7              magicaxis_2.4.5         coop_0.6-3             </span></span>
 <span><span class="co">#&gt;  [25] purrr_1.0.2             xfun_0.49               zlibbioc_1.48.2        </span></span>
 <span><span class="co">#&gt;  [28] cachem_1.1.0            celestial_1.4.6         jsonlite_1.8.9         </span></span>
-<span><span class="co">#&gt;  [31] SnowballC_0.7.1         later_1.3.2             DelayedArray_0.28.0    </span></span>
+<span><span class="co">#&gt;  [31] SnowballC_0.7.1         later_1.4.1             DelayedArray_0.28.0    </span></span>
 <span><span class="co">#&gt;  [34] BiocParallel_1.36.0     parallel_4.3.0          sets_1.0-25            </span></span>
 <span><span class="co">#&gt;  [37] cluster_2.1.4           R6_2.5.1                stringi_1.8.4          </span></span>
 <span><span class="co">#&gt;  [40] bslib_0.8.0             RColorBrewer_1.1-3      qs_0.27.2              </span></span>
 <span><span class="co">#&gt;  [43] limma_3.58.1            boot_1.3-28.1           jquerylib_0.1.4        </span></span>
-<span><span class="co">#&gt;  [46] Rcpp_1.0.13-1           knitr_1.48              downloader_0.4         </span></span>
-<span><span class="co">#&gt;  [49] httpuv_1.6.15           Matrix_1.6-5            igraph_2.1.1           </span></span>
+<span><span class="co">#&gt;  [46] Rcpp_1.0.13-1           knitr_1.49              downloader_0.4         </span></span>
+<span><span class="co">#&gt;  [49] httpuv_1.6.15           Matrix_1.6-5            igraph_2.1.2           </span></span>
 <span><span class="co">#&gt;  [52] tidyselect_1.2.1        abind_1.4-8             yaml_2.3.10            </span></span>
 <span><span class="co">#&gt;  [55] stringfish_0.16.0       gplots_3.2.0            codetools_0.2-19       </span></span>
 <span><span class="co">#&gt;  [58] plyr_1.8.9              lattice_0.21-8          tibble_3.2.1           </span></span>
@@ -1319,8 +1319,8 @@ <h2 id="references">References<a class="anchor" aria-label="anchor" href="#refer
 <span><span class="co">#&gt;  [76] RCurl_1.98-1.16         ggplot2_3.5.1           munsell_0.5.1          </span></span>
 <span><span class="co">#&gt;  [79] scales_1.3.0            RApiSerialize_0.1.4     gtools_3.9.5           </span></span>
 <span><span class="co">#&gt;  [82] xtable_1.8-4            marray_1.80.0           glue_1.8.0             </span></span>
-<span><span class="co">#&gt;  [85] slam_0.1-54             mapproj_1.2.11          tools_4.3.0            </span></span>
-<span><span class="co">#&gt;  [88] data.table_1.16.2       gDRutils_1.5.2          fgsea_1.28.0           </span></span>
+<span><span class="co">#&gt;  [85] slam_0.1-55             mapproj_1.2.11          tools_4.3.0            </span></span>
+<span><span class="co">#&gt;  [88] data.table_1.16.4       gDRutils_1.5.3          fgsea_1.28.0           </span></span>
 <span><span class="co">#&gt;  [91] RANN_2.6.2              fs_1.6.5                visNetwork_2.1.2       </span></span>
 <span><span class="co">#&gt;  [94] fastmatch_1.1-4         cowplot_1.1.3           grid_4.3.0             </span></span>
 <span><span class="co">#&gt;  [97] plotrix_3.8-4           NISTunits_1.0.1         colorspace_2.1-1       </span></span>
diff --git a/docs/articles/ConvertingPharmacoSetToGDR.html b/docs/articles/ConvertingPharmacoSetToGDR.html
index 321398c..2367148 100644
--- a/docs/articles/ConvertingPharmacoSetToGDR.html
+++ b/docs/articles/ConvertingPharmacoSetToGDR.html
@@ -26,7 +26,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">gDRimport</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -306,7 +306,7 @@ <h2 class="unnumbered" id="sessioninfo">SessionInfo<a class="anchor" aria-label=
 <span><span class="co">#&gt; [8] base     </span></span>
 <span><span class="co">#&gt; </span></span>
 <span><span class="co">#&gt; other attached packages:</span></span>
-<span><span class="co">#&gt;  [1] gDRimport_1.5.2             PharmacoGx_3.6.0           </span></span>
+<span><span class="co">#&gt;  [1] gDRimport_1.5.3             PharmacoGx_3.6.0           </span></span>
 <span><span class="co">#&gt;  [3] CoreGx_2.6.1                SummarizedExperiment_1.32.0</span></span>
 <span><span class="co">#&gt;  [5] Biobase_2.62.0              GenomicRanges_1.54.1       </span></span>
 <span><span class="co">#&gt;  [7] GenomeInfoDb_1.38.8         IRanges_2.36.0             </span></span>
@@ -326,7 +326,7 @@ <h2 class="unnumbered" id="sessioninfo">SessionInfo<a class="anchor" aria-label=
 <span><span class="co">#&gt;  [19] KernSmooth_2.23-20          bslib_0.8.0                </span></span>
 <span><span class="co">#&gt;  [21] htmlwidgets_1.6.4           desc_1.4.3                 </span></span>
 <span><span class="co">#&gt;  [23] plyr_1.8.9                  testthat_3.2.1             </span></span>
-<span><span class="co">#&gt;  [25] cachem_1.1.0                igraph_2.1.1               </span></span>
+<span><span class="co">#&gt;  [25] cachem_1.1.0                igraph_2.1.2               </span></span>
 <span><span class="co">#&gt;  [27] mime_0.12                   lifecycle_1.0.4            </span></span>
 <span><span class="co">#&gt;  [29] piano_2.18.0                pkgconfig_2.0.3            </span></span>
 <span><span class="co">#&gt;  [31] Matrix_1.6-5                R6_2.5.1                   </span></span>
@@ -338,26 +338,26 @@ <h2 class="unnumbered" id="sessioninfo">SessionInfo<a class="anchor" aria-label=
 <span><span class="co">#&gt;  [43] abind_1.4-8                 coop_0.6-3                 </span></span>
 <span><span class="co">#&gt;  [45] compiler_4.3.0              downloader_0.4             </span></span>
 <span><span class="co">#&gt;  [47] marray_1.80.0               backports_1.5.0            </span></span>
-<span><span class="co">#&gt;  [49] BiocParallel_1.36.0         gDRutils_1.5.2             </span></span>
+<span><span class="co">#&gt;  [49] BiocParallel_1.36.0         gDRutils_1.5.3             </span></span>
 <span><span class="co">#&gt;  [51] bench_1.1.3                 qs_0.27.2                  </span></span>
-<span><span class="co">#&gt;  [53] gplots_3.2.0                maps_3.4.2                 </span></span>
+<span><span class="co">#&gt;  [53] gplots_3.2.0                maps_3.4.2.1               </span></span>
 <span><span class="co">#&gt;  [55] MASS_7.3-58.4               DelayedArray_0.28.0        </span></span>
 <span><span class="co">#&gt;  [57] gtools_3.9.5                caTools_1.18.3             </span></span>
 <span><span class="co">#&gt;  [59] tools_4.3.0                 NISTunits_1.0.1            </span></span>
-<span><span class="co">#&gt;  [61] httpuv_1.6.15               relations_0.6-13           </span></span>
-<span><span class="co">#&gt;  [63] glue_1.8.0                  promises_1.3.0             </span></span>
+<span><span class="co">#&gt;  [61] httpuv_1.6.15               relations_0.6-14           </span></span>
+<span><span class="co">#&gt;  [63] glue_1.8.0                  promises_1.3.2             </span></span>
 <span><span class="co">#&gt;  [65] grid_4.3.0                  checkmate_2.3.2            </span></span>
 <span><span class="co">#&gt;  [67] cluster_2.1.4               reshape2_1.4.4             </span></span>
 <span><span class="co">#&gt;  [69] fgsea_1.28.0                generics_0.1.3             </span></span>
 <span><span class="co">#&gt;  [71] gtable_0.3.6                sm_2.2-6.0                 </span></span>
-<span><span class="co">#&gt;  [73] data.table_1.16.2           RApiSerialize_0.1.4        </span></span>
+<span><span class="co">#&gt;  [73] data.table_1.16.4           RApiSerialize_0.1.4        </span></span>
 <span><span class="co">#&gt;  [75] stringfish_0.16.0           utf8_1.2.4                 </span></span>
 <span><span class="co">#&gt;  [77] XVector_0.42.0              RANN_2.6.2                 </span></span>
 <span><span class="co">#&gt;  [79] pillar_1.9.0                stringr_1.5.1              </span></span>
 <span><span class="co">#&gt;  [81] limma_3.58.1                BumpyMatrix_1.10.0         </span></span>
-<span><span class="co">#&gt;  [83] later_1.3.2                 dplyr_1.1.4                </span></span>
+<span><span class="co">#&gt;  [83] later_1.4.1                 dplyr_1.1.4                </span></span>
 <span><span class="co">#&gt;  [85] lattice_0.21-8              tidyselect_1.2.1           </span></span>
-<span><span class="co">#&gt;  [87] knitr_1.48                  xfun_0.49                  </span></span>
+<span><span class="co">#&gt;  [87] knitr_1.49                  xfun_0.49                  </span></span>
 <span><span class="co">#&gt;  [89] shinydashboard_0.7.2        statmod_1.5.0              </span></span>
 <span><span class="co">#&gt;  [91] brio_1.1.4                  DT_0.33                    </span></span>
 <span><span class="co">#&gt;  [93] visNetwork_2.1.2            stringi_1.8.4              </span></span>
@@ -371,7 +371,7 @@ <h2 class="unnumbered" id="sessioninfo">SessionInfo<a class="anchor" aria-label=
 <span><span class="co">#&gt; [109] parallel_4.3.0              sets_1.0-25                </span></span>
 <span><span class="co">#&gt; [111] pkgdown_2.0.7               ggplot2_3.5.1              </span></span>
 <span><span class="co">#&gt; [113] assertthat_0.2.1            bitops_1.0-9               </span></span>
-<span><span class="co">#&gt; [115] slam_0.1-54                 celestial_1.4.6            </span></span>
+<span><span class="co">#&gt; [115] slam_0.1-55                 celestial_1.4.6            </span></span>
 <span><span class="co">#&gt; [117] scales_1.3.0                purrr_1.0.2                </span></span>
 <span><span class="co">#&gt; [119] crayon_1.5.3                rlang_1.1.4                </span></span>
 <span><span class="co">#&gt; [121] cowplot_1.1.3               fastmatch_1.1-4            </span></span>
diff --git a/docs/articles/gDRimport.html b/docs/articles/gDRimport.html
index 14494eb..2b70b09 100644
--- a/docs/articles/gDRimport.html
+++ b/docs/articles/gDRimport.html
@@ -26,7 +26,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">gDRimport</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -272,7 +272,7 @@ <h2 class="unnumbered" id="sessioninfo">SessionInfo<a class="anchor" aria-label=
 <span><span class="co">## [1] stats     graphics  grDevices utils     datasets  methods   base     </span></span>
 <span><span class="co">## </span></span>
 <span><span class="co">## other attached packages:</span></span>
-<span><span class="co">## [1] gDRimport_1.5.2  BiocStyle_2.30.0</span></span>
+<span><span class="co">## [1] gDRimport_1.5.3  BiocStyle_2.30.0</span></span>
 <span><span class="co">## </span></span>
 <span><span class="co">## loaded via a namespace (and not attached):</span></span>
 <span><span class="co">##  [1] SummarizedExperiment_1.32.0 xfun_0.49                  </span></span>
@@ -281,9 +281,9 @@ <h2 class="unnumbered" id="sessioninfo">SessionInfo<a class="anchor" aria-label=
 <span><span class="co">##  [7] tools_4.3.0                 bitops_1.0-9               </span></span>
 <span><span class="co">##  [9] stats4_4.3.0                tibble_3.2.1               </span></span>
 <span><span class="co">## [11] fansi_1.0.6                 pkgconfig_2.0.3            </span></span>
-<span><span class="co">## [13] Matrix_1.6-5                data.table_1.16.2          </span></span>
+<span><span class="co">## [13] Matrix_1.6-5                data.table_1.16.4          </span></span>
 <span><span class="co">## [15] checkmate_2.3.2             desc_1.4.3                 </span></span>
-<span><span class="co">## [17] S4Vectors_0.40.2            gDRutils_1.5.2             </span></span>
+<span><span class="co">## [17] S4Vectors_0.40.2            gDRutils_1.5.3             </span></span>
 <span><span class="co">## [19] rematch_2.0.0               readxl_1.4.3               </span></span>
 <span><span class="co">## [21] assertthat_0.2.1            lifecycle_1.0.4            </span></span>
 <span><span class="co">## [23] GenomeInfoDbData_1.2.11     compiler_4.3.0             </span></span>
@@ -303,7 +303,7 @@ <h2 class="unnumbered" id="sessioninfo">SessionInfo<a class="anchor" aria-label=
 <span><span class="co">## [51] XVector_0.42.0              matrixStats_1.4.1          </span></span>
 <span><span class="co">## [53] futile.logger_1.4.3         cellranger_1.1.0           </span></span>
 <span><span class="co">## [55] ragg_1.2.7                  memoise_2.0.1              </span></span>
-<span><span class="co">## [57] evaluate_1.0.1              knitr_1.48                 </span></span>
+<span><span class="co">## [57] evaluate_1.0.1              knitr_1.49                 </span></span>
 <span><span class="co">## [59] GenomicRanges_1.54.1        IRanges_2.36.0             </span></span>
 <span><span class="co">## [61] rlang_1.1.4                 futile.options_1.0.1       </span></span>
 <span><span class="co">## [63] glue_1.8.0                  BiocManager_1.30.22        </span></span>
diff --git a/docs/articles/index.html b/docs/articles/index.html
index 9170e64..3da5d15 100644
--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">gDRimport</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/authors.html b/docs/authors.html
index 3172db8..c1f1842 100644
--- a/docs/authors.html
+++ b/docs/authors.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="index.html">gDRimport</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/index.html b/docs/index.html
index 1bfac15..227a25a 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -26,7 +26,7 @@
     
     <a class="navbar-brand me-2" href="index.html">gDRimport</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/news/index.html b/docs/news/index.html
index e54f077..47e559c 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">gDRimport</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -54,6 +54,10 @@
       <small>Source: <a href="https://github.com/gdrplatform/gDRimport/blob/HEAD/NEWS.md" class="external-link"><code>NEWS.md</code></a></small>
     </div>
 
+    <div class="section level2">
+<h2 class="pkg-version" data-toc-text="1.5.3" id="gdrimport-153---2024-12-04">gDRimport 1.5.3 - 2024-12-04<a class="anchor" aria-label="anchor" href="#gdrimport-153---2024-12-04"></a></h2>
+<ul><li>support old private PRISM data format</li>
+</ul></div>
     <div class="section level2">
 <h2 class="pkg-version" data-toc-text="1.5.2" id="gdrimport-152---2024-11-06">gDRimport 1.5.2 - 2024-11-06<a class="anchor" aria-label="anchor" href="#gdrimport-152---2024-11-06"></a></h2>
 <ul><li>fix invalid moa for PRISM data</li>
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index fed1cd9..5a21e9b 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -5,7 +5,7 @@ articles:
   ConvertingMAEtoPharmacoSet: ConvertingMAEtoPharmacoSet.html
   ConvertingPharmacoSetToGDR: ConvertingPharmacoSetToGDR.html
   gDRimport: gDRimport.html
-last_built: 2024-11-07T10:36Z
+last_built: 2024-12-09T10:52Z
 urls:
   reference: https://gdrplatform.github.io/gDRimport/reference
   article: https://gdrplatform.github.io/gDRimport/articles
diff --git a/docs/reference/are_template_sheets_valid.html b/docs/reference/are_template_sheets_valid.html
index 2cd27bc..ff99acc 100644
--- a/docs/reference/are_template_sheets_valid.html
+++ b/docs/reference/are_template_sheets_valid.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">gDRimport</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/check_metadata_against_spaces.html b/docs/reference/check_metadata_against_spaces.html
index ca20447..d4071bb 100644
--- a/docs/reference/check_metadata_against_spaces.html
+++ b/docs/reference/check_metadata_against_spaces.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">gDRimport</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/check_metadata_field_names.html b/docs/reference/check_metadata_field_names.html
index fd059d2..a2b34cb 100644
--- a/docs/reference/check_metadata_field_names.html
+++ b/docs/reference/check_metadata_field_names.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">gDRimport</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/check_metadata_headers.html b/docs/reference/check_metadata_headers.html
index 6b69b79..a2e4e07 100644
--- a/docs/reference/check_metadata_headers.html
+++ b/docs/reference/check_metadata_headers.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">gDRimport</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/check_metadata_names.html b/docs/reference/check_metadata_names.html
index d1f0e41..ff925e6 100644
--- a/docs/reference/check_metadata_names.html
+++ b/docs/reference/check_metadata_names.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">gDRimport</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/check_metadata_req_col_names.html b/docs/reference/check_metadata_req_col_names.html
index d1b87fe..ad9aece 100644
--- a/docs/reference/check_metadata_req_col_names.html
+++ b/docs/reference/check_metadata_req_col_names.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">gDRimport</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/convert_LEVEL5_prism_to_gDR_input.html b/docs/reference/convert_LEVEL5_prism_to_gDR_input.html
index 5f17794..05a2c67 100644
--- a/docs/reference/convert_LEVEL5_prism_to_gDR_input.html
+++ b/docs/reference/convert_LEVEL5_prism_to_gDR_input.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">gDRimport</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -85,10 +85,10 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
     <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span> <span class="va">prism_data</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.file.html" class="external-link">system.file</a></span><span class="op">(</span><span class="st">"testdata/prism_sa.csv"</span>, package <span class="op">=</span> <span class="st">"gDRimport"</span><span class="op">)</span></span></span>
 <span class="r-in"><span> <span class="fu">convert_LEVEL5_prism_to_gDR_input</span><span class="op">(</span><span class="va">prism_data</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>         clid Duration ReadoutValue BackgroundValue      Gnumber Concentration</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>       &lt;char&gt;    &lt;num&gt;        &lt;num&gt;           &lt;num&gt;       &lt;char&gt;         &lt;num&gt;</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 1: some_clid      120         1.03               0 some_gnumber      0.003201</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2: some_clid      120         1.00               0      vehicle      0.000000</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>         clid Duration ReadoutValue BackgroundValue     Gnumber Concentration</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>       &lt;char&gt;    &lt;num&gt;        &lt;num&gt;           &lt;num&gt;      &lt;char&gt;         &lt;num&gt;</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1: some_clid      120         1.03               0 someGnumber      0.003201</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2: some_clid      120         1.00               0     vehicle      0.000000</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    masked</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    &lt;lgcl&gt;</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> 1:  FALSE</span>
diff --git a/docs/reference/convert_LEVEL6_prism_to_gDR_input.html b/docs/reference/convert_LEVEL6_prism_to_gDR_input.html
index 3caee7f..88e4cc9 100644
--- a/docs/reference/convert_LEVEL6_prism_to_gDR_input.html
+++ b/docs/reference/convert_LEVEL6_prism_to_gDR_input.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">gDRimport</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/convert_MAE_to_PSet.html b/docs/reference/convert_MAE_to_PSet.html
index afe46c7..8c337b3 100644
--- a/docs/reference/convert_MAE_to_PSet.html
+++ b/docs/reference/convert_MAE_to_PSet.html
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">gDRimport</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -99,7 +99,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span><span class="fu">convert_MAE_to_PSet</span><span class="op">(</span><span class="va">mae</span>, <span class="st">"my_pset"</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> &lt;PharmacoSet&gt;</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Name:  my_pset </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Date Created:  Thu Nov  7 10:36:41 2024 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Date Created:  Mon Dec  9 10:53:08 2024 </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Number of samples:  10 </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Molecular profiles:</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    A MultiAssayExperiment object of 1 listed</span>
diff --git a/docs/reference/convert_pset_to_df.html b/docs/reference/convert_pset_to_df.html
index 4bcfd24..3ef950e 100644
--- a/docs/reference/convert_pset_to_df.html
+++ b/docs/reference/convert_pset_to_df.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">gDRimport</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/correct_template_sheets.html b/docs/reference/correct_template_sheets.html
index 345e0e6..e7c90da 100644
--- a/docs/reference/correct_template_sheets.html
+++ b/docs/reference/correct_template_sheets.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">gDRimport</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/detect_file_format.html b/docs/reference/detect_file_format.html
index fa8351e..da35af4 100644
--- a/docs/reference/detect_file_format.html
+++ b/docs/reference/detect_file_format.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">gDRimport</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/dot-check_against_single_template_sheet.html b/docs/reference/dot-check_against_single_template_sheet.html
index 8b5715a..d6ad80a 100644
--- a/docs/reference/dot-check_against_single_template_sheet.html
+++ b/docs/reference/dot-check_against_single_template_sheet.html
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">gDRimport</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/dot-check_file_structure.html b/docs/reference/dot-check_file_structure.html
index a6f692c..dab3aa0 100644
--- a/docs/reference/dot-check_file_structure.html
+++ b/docs/reference/dot-check_file_structure.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">gDRimport</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/dot-createPseudoData.html b/docs/reference/dot-createPseudoData.html
index de6f157..c93ce71 100644
--- a/docs/reference/dot-createPseudoData.html
+++ b/docs/reference/dot-createPseudoData.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">gDRimport</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/dot-extractDoseResponse.html b/docs/reference/dot-extractDoseResponse.html
index 0db870c..28c947e 100644
--- a/docs/reference/dot-extractDoseResponse.html
+++ b/docs/reference/dot-extractDoseResponse.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">gDRimport</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/dot-extract_or_create_assay.html b/docs/reference/dot-extract_or_create_assay.html
index f45c4c5..081f8f9 100644
--- a/docs/reference/dot-extract_or_create_assay.html
+++ b/docs/reference/dot-extract_or_create_assay.html
@@ -20,7 +20,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">gDRimport</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/dot-fill_empty_wells.html b/docs/reference/dot-fill_empty_wells.html
index 631121d..5ccef2e 100644
--- a/docs/reference/dot-fill_empty_wells.html
+++ b/docs/reference/dot-fill_empty_wells.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">gDRimport</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/dot-get_plate_size.html b/docs/reference/dot-get_plate_size.html
index 31980f5..2d3dc5d 100644
--- a/docs/reference/dot-get_plate_size.html
+++ b/docs/reference/dot-get_plate_size.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">gDRimport</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/dot-removeNegatives.html b/docs/reference/dot-removeNegatives.html
index 8f9b1ca..09262e7 100644
--- a/docs/reference/dot-removeNegatives.html
+++ b/docs/reference/dot-removeNegatives.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">gDRimport</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/dot-standardize_untreated_values.html b/docs/reference/dot-standardize_untreated_values.html
index 7f11699..a0aab1b 100644
--- a/docs/reference/dot-standardize_untreated_values.html
+++ b/docs/reference/dot-standardize_untreated_values.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">gDRimport</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/enhance_raw_edited_EnVision_df.html b/docs/reference/enhance_raw_edited_EnVision_df.html
index 5a9379a..4cf8142 100644
--- a/docs/reference/enhance_raw_edited_EnVision_df.html
+++ b/docs/reference/enhance_raw_edited_EnVision_df.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">gDRimport</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/fix_typos_with_reference.html b/docs/reference/fix_typos_with_reference.html
index b2e33c2..04d3618 100644
--- a/docs/reference/fix_typos_with_reference.html
+++ b/docs/reference/fix_typos_with_reference.html
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">gDRimport</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/gDRimport-package.html b/docs/reference/gDRimport-package.html
index 34514ac..443c65d 100644
--- a/docs/reference/gDRimport-package.html
+++ b/docs/reference/gDRimport-package.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">gDRimport</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/gdr_test_data-class.html b/docs/reference/gdr_test_data-class.html
index d80b5c5..b14027f 100644
--- a/docs/reference/gdr_test_data-class.html
+++ b/docs/reference/gdr_test_data-class.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">gDRimport</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/getPSet.html b/docs/reference/getPSet.html
index 10ebb59..d21001f 100644
--- a/docs/reference/getPSet.html
+++ b/docs/reference/getPSet.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">gDRimport</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/get_EnVision_properties.html b/docs/reference/get_EnVision_properties.html
index e1d8b87..632882d 100644
--- a/docs/reference/get_EnVision_properties.html
+++ b/docs/reference/get_EnVision_properties.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">gDRimport</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/get_df_from_raw_edited_EnVision_df.html b/docs/reference/get_df_from_raw_edited_EnVision_df.html
index 02eee1e..b78f0ea 100644
--- a/docs/reference/get_df_from_raw_edited_EnVision_df.html
+++ b/docs/reference/get_df_from_raw_edited_EnVision_df.html
@@ -14,7 +14,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">gDRimport</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/get_df_from_raw_unedited_EnVision_df.html b/docs/reference/get_df_from_raw_unedited_EnVision_df.html
index 961f57c..c7794e4 100644
--- a/docs/reference/get_df_from_raw_unedited_EnVision_df.html
+++ b/docs/reference/get_df_from_raw_unedited_EnVision_df.html
@@ -14,7 +14,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">gDRimport</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/get_excel_sheet_names.html b/docs/reference/get_excel_sheet_names.html
index d012326..6f251e4 100644
--- a/docs/reference/get_excel_sheet_names.html
+++ b/docs/reference/get_excel_sheet_names.html
@@ -14,7 +14,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">gDRimport</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/get_exception_data.html b/docs/reference/get_exception_data.html
index 1bc7405..ea01b28 100644
--- a/docs/reference/get_exception_data.html
+++ b/docs/reference/get_exception_data.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">gDRimport</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/get_expected_template_sheets.html b/docs/reference/get_expected_template_sheets.html
index 0735a26..9155dc4 100644
--- a/docs/reference/get_expected_template_sheets.html
+++ b/docs/reference/get_expected_template_sheets.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">gDRimport</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/get_plate_info_from_template_xlsx.html b/docs/reference/get_plate_info_from_template_xlsx.html
index 7f3258e..4599327 100644
--- a/docs/reference/get_plate_info_from_template_xlsx.html
+++ b/docs/reference/get_plate_info_from_template_xlsx.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">gDRimport</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/get_test_D300_data.html b/docs/reference/get_test_D300_data.html
index bc44e2a..97f9d67 100644
--- a/docs/reference/get_test_D300_data.html
+++ b/docs/reference/get_test_D300_data.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">gDRimport</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/get_test_EnVision_data.html b/docs/reference/get_test_EnVision_data.html
index f28d655..61457da 100644
--- a/docs/reference/get_test_EnVision_data.html
+++ b/docs/reference/get_test_EnVision_data.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">gDRimport</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/get_test_Tecan_data.html b/docs/reference/get_test_Tecan_data.html
index bb95c59..dd4e07e 100644
--- a/docs/reference/get_test_Tecan_data.html
+++ b/docs/reference/get_test_Tecan_data.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">gDRimport</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/get_test_data.html b/docs/reference/get_test_data.html
index bded454..a97558d 100644
--- a/docs/reference/get_test_data.html
+++ b/docs/reference/get_test_data.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">gDRimport</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/get_test_tsv_data.html b/docs/reference/get_test_tsv_data.html
index 86687ba..9a0f097 100644
--- a/docs/reference/get_test_tsv_data.html
+++ b/docs/reference/get_test_tsv_data.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">gDRimport</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/get_xl_sheets.html b/docs/reference/get_xl_sheets.html
index 973640d..4b708c5 100644
--- a/docs/reference/get_xl_sheets.html
+++ b/docs/reference/get_xl_sheets.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">gDRimport</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/import_D300.html b/docs/reference/import_D300.html
index b0a6738..a398981 100644
--- a/docs/reference/import_D300.html
+++ b/docs/reference/import_D300.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">gDRimport</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/index.html b/docs/reference/index.html
index 22594fe..021bc93 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">gDRimport</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/is_readable_v.html b/docs/reference/is_readable_v.html
index 7d86b07..dbb6b70 100644
--- a/docs/reference/is_readable_v.html
+++ b/docs/reference/is_readable_v.html
@@ -14,7 +14,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">gDRimport</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/load_data.html b/docs/reference/load_data.html
index 781645c..80d9eb5 100644
--- a/docs/reference/load_data.html
+++ b/docs/reference/load_data.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">gDRimport</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -100,12 +100,12 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
     <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span> <span class="va">td</span> <span class="op">&lt;-</span> <span class="fu"><a href="get_test_data.html">get_test_data</a></span><span class="op">(</span><span class="op">)</span></span></span>
 <span class="r-in"><span> <span class="va">l_tbl</span> <span class="op">&lt;-</span> <span class="fu">load_data</span><span class="op">(</span><span class="fu"><a href="manifest_path-method.html">manifest_path</a></span><span class="op">(</span><span class="va">td</span><span class="op">)</span>, <span class="fu"><a href="template_path-method.html">template_path</a></span><span class="op">(</span><span class="va">td</span><span class="op">)</span>, <span class="fu"><a href="result_path-method.html">result_path</a></span><span class="op">(</span><span class="va">td</span><span class="op">)</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> INFO [2024-11-07 10:36:50] Manifest loaded successfully</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> INFO [2024-11-07 10:36:50] Reading Template_7daytreated.xlsx with load_templates_xlsx</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> INFO [2024-11-07 10:36:50] Loading Template_7daytreated.xlsx</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> INFO [2024-11-07 10:36:50] Loading Template_Untreated.xlsx</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> INFO [2024-11-07 10:36:50] Templates loaded successfully!</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> INFO [2024-11-07 10:36:50] Reading file /usr/local/lib/R/site-library/gDRimport/extdata/data1/RawData_day0.xlsx, sheet Readout_0077vs0068_day7</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> INFO [2024-12-09 10:53:16] Manifest loaded successfully</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> INFO [2024-12-09 10:53:16] Reading Template_7daytreated.xlsx with load_templates_xlsx</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> INFO [2024-12-09 10:53:16] Loading Template_7daytreated.xlsx</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> INFO [2024-12-09 10:53:17] Loading Template_Untreated.xlsx</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> INFO [2024-12-09 10:53:17] Templates loaded successfully!</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> INFO [2024-12-09 10:53:17] Reading file /usr/local/lib/R/site-library/gDRimport/extdata/data1/RawData_day0.xlsx, sheet Readout_0077vs0068_day7</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> New names:</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">•</span> `` -&gt; `...1`</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">•</span> `` -&gt; `...2`</span>
@@ -132,14 +132,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">•</span> `` -&gt; `...23`</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">•</span> `` -&gt; `...24`</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">•</span> `` -&gt; `...25`</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> INFO [2024-11-07 10:36:50] Plate 201904190a read; 384 wells</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> INFO [2024-11-07 10:36:50] Plate 201904190b read; 384 wells</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> INFO [2024-11-07 10:36:50] Plate 201904190c read; 384 wells</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> INFO [2024-11-07 10:36:50] Plate 201904190d read; 384 wells</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> INFO [2024-11-07 10:36:50] Plate 201904190e read; 384 wells</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> INFO [2024-11-07 10:36:50] Plate 201904190f read; 384 wells</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> INFO [2024-11-07 10:36:50] File done</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> INFO [2024-11-07 10:36:50] Reading file /usr/local/lib/R/site-library/gDRimport/extdata/data1/RawData_day7.xlsx, sheet Readout_0077vs0068_day7</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> INFO [2024-12-09 10:53:17] Plate 201904190a read; 384 wells</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> INFO [2024-12-09 10:53:17] Plate 201904190b read; 384 wells</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> INFO [2024-12-09 10:53:17] Plate 201904190c read; 384 wells</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> INFO [2024-12-09 10:53:17] Plate 201904190d read; 384 wells</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> INFO [2024-12-09 10:53:17] Plate 201904190e read; 384 wells</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> INFO [2024-12-09 10:53:17] Plate 201904190f read; 384 wells</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> INFO [2024-12-09 10:53:17] File done</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> INFO [2024-12-09 10:53:17] Reading file /usr/local/lib/R/site-library/gDRimport/extdata/data1/RawData_day7.xlsx, sheet Readout_0077vs0068_day7</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> New names:</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">•</span> `` -&gt; `...1`</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">•</span> `` -&gt; `...2`</span>
@@ -166,13 +166,13 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">•</span> `` -&gt; `...23`</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">•</span> `` -&gt; `...24`</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">•</span> `` -&gt; `...25`</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> INFO [2024-11-07 10:36:51] Plate 201904197a read; 384 wells</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> INFO [2024-11-07 10:36:51] Plate 201904197b read; 384 wells</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> INFO [2024-11-07 10:36:51] Plate 201904197c read; 384 wells</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> INFO [2024-11-07 10:36:51] Plate 201904197d read; 384 wells</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> INFO [2024-11-07 10:36:51] Plate 201904197e read; 384 wells</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> INFO [2024-11-07 10:36:51] Plate 201904197f read; 384 wells</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> INFO [2024-11-07 10:36:51] File done</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> INFO [2024-12-09 10:53:17] Plate 201904197a read; 384 wells</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> INFO [2024-12-09 10:53:17] Plate 201904197b read; 384 wells</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> INFO [2024-12-09 10:53:17] Plate 201904197c read; 384 wells</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> INFO [2024-12-09 10:53:17] Plate 201904197d read; 384 wells</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> INFO [2024-12-09 10:53:17] Plate 201904197e read; 384 wells</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> INFO [2024-12-09 10:53:17] Plate 201904197f read; 384 wells</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> INFO [2024-12-09 10:53:17] File done</span>
 <span class="r-in"><span></span></span>
 </code></pre></div>
     </div>
diff --git a/docs/reference/load_manifest.html b/docs/reference/load_manifest.html
index 09e64d8..bdd3843 100644
--- a/docs/reference/load_manifest.html
+++ b/docs/reference/load_manifest.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">gDRimport</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -81,7 +81,7 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
     <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span> <span class="va">td</span> <span class="op">&lt;-</span> <span class="fu"><a href="get_test_data.html">get_test_data</a></span><span class="op">(</span><span class="op">)</span></span></span>
 <span class="r-in"><span> <span class="va">ml</span> <span class="op">&lt;-</span> <span class="fu">load_manifest</span><span class="op">(</span><span class="fu"><a href="manifest_path-method.html">manifest_path</a></span><span class="op">(</span><span class="va">td</span><span class="op">)</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> INFO [2024-11-07 10:36:51] Manifest loaded successfully</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> INFO [2024-12-09 10:53:17] Manifest loaded successfully</span>
 <span class="r-in"><span></span></span>
 </code></pre></div>
     </div>
diff --git a/docs/reference/load_results.html b/docs/reference/load_results.html
index 9d7ebdb..3a7cc88 100644
--- a/docs/reference/load_results.html
+++ b/docs/reference/load_results.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">gDRimport</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -94,7 +94,7 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
     <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span> <span class="va">td</span> <span class="op">&lt;-</span> <span class="fu"><a href="get_test_data.html">get_test_data</a></span><span class="op">(</span><span class="op">)</span></span></span>
 <span class="r-in"><span> <span class="va">r_df</span> <span class="op">&lt;-</span> <span class="fu">load_results</span><span class="op">(</span><span class="fu"><a href="result_path-method.html">result_path</a></span><span class="op">(</span><span class="va">td</span><span class="op">)</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> INFO [2024-11-07 10:36:51] Reading file /usr/local/lib/R/site-library/gDRimport/extdata/data1/RawData_day0.xlsx, sheet Readout_0077vs0068_day7</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> INFO [2024-12-09 10:53:17] Reading file /usr/local/lib/R/site-library/gDRimport/extdata/data1/RawData_day0.xlsx, sheet Readout_0077vs0068_day7</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> New names:</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">•</span> `` -&gt; `...1`</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">•</span> `` -&gt; `...2`</span>
@@ -121,14 +121,14 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">•</span> `` -&gt; `...23`</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">•</span> `` -&gt; `...24`</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">•</span> `` -&gt; `...25`</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> INFO [2024-11-07 10:36:51] Plate 1 read; 384 wells</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> INFO [2024-11-07 10:36:51] Plate 2 read; 384 wells</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> INFO [2024-11-07 10:36:51] Plate 3 read; 384 wells</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> INFO [2024-11-07 10:36:51] Plate 4 read; 384 wells</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> INFO [2024-11-07 10:36:51] Plate 5 read; 384 wells</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> INFO [2024-11-07 10:36:51] Plate 6 read; 384 wells</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> INFO [2024-11-07 10:36:51] File done</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> INFO [2024-11-07 10:36:51] Reading file /usr/local/lib/R/site-library/gDRimport/extdata/data1/RawData_day7.xlsx, sheet Readout_0077vs0068_day7</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> INFO [2024-12-09 10:53:18] Plate 1 read; 384 wells</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> INFO [2024-12-09 10:53:18] Plate 2 read; 384 wells</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> INFO [2024-12-09 10:53:18] Plate 3 read; 384 wells</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> INFO [2024-12-09 10:53:18] Plate 4 read; 384 wells</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> INFO [2024-12-09 10:53:18] Plate 5 read; 384 wells</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> INFO [2024-12-09 10:53:18] Plate 6 read; 384 wells</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> INFO [2024-12-09 10:53:18] File done</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> INFO [2024-12-09 10:53:18] Reading file /usr/local/lib/R/site-library/gDRimport/extdata/data1/RawData_day7.xlsx, sheet Readout_0077vs0068_day7</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> New names:</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">•</span> `` -&gt; `...1`</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">•</span> `` -&gt; `...2`</span>
@@ -155,13 +155,13 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">•</span> `` -&gt; `...23`</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">•</span> `` -&gt; `...24`</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">•</span> `` -&gt; `...25`</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> INFO [2024-11-07 10:36:51] Plate 1 read; 384 wells</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> INFO [2024-11-07 10:36:51] Plate 2 read; 384 wells</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> INFO [2024-11-07 10:36:51] Plate 3 read; 384 wells</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> INFO [2024-11-07 10:36:51] Plate 4 read; 384 wells</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> INFO [2024-11-07 10:36:51] Plate 5 read; 384 wells</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> INFO [2024-11-07 10:36:51] Plate 6 read; 384 wells</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> INFO [2024-11-07 10:36:51] File done</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> INFO [2024-12-09 10:53:18] Plate 1 read; 384 wells</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> INFO [2024-12-09 10:53:18] Plate 2 read; 384 wells</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> INFO [2024-12-09 10:53:18] Plate 3 read; 384 wells</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> INFO [2024-12-09 10:53:18] Plate 4 read; 384 wells</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> INFO [2024-12-09 10:53:18] Plate 5 read; 384 wells</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> INFO [2024-12-09 10:53:18] Plate 6 read; 384 wells</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> INFO [2024-12-09 10:53:18] File done</span>
 <span class="r-in"><span></span></span>
 </code></pre></div>
     </div>
diff --git a/docs/reference/load_results_EnVision.html b/docs/reference/load_results_EnVision.html
index d6a3ff1..bb4e687 100644
--- a/docs/reference/load_results_EnVision.html
+++ b/docs/reference/load_results_EnVision.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">gDRimport</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/load_results_Tecan.html b/docs/reference/load_results_Tecan.html
index fe23a45..4f9c4b1 100644
--- a/docs/reference/load_results_Tecan.html
+++ b/docs/reference/load_results_Tecan.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">gDRimport</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/load_results_tsv.html b/docs/reference/load_results_tsv.html
index 61607ab..3f1c336 100644
--- a/docs/reference/load_results_tsv.html
+++ b/docs/reference/load_results_tsv.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">gDRimport</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/load_templates.html b/docs/reference/load_templates.html
index 1ac908e..48c3286 100644
--- a/docs/reference/load_templates.html
+++ b/docs/reference/load_templates.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">gDRimport</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -82,10 +82,10 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
     <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span> <span class="va">td</span> <span class="op">&lt;-</span> <span class="fu"><a href="get_test_data.html">get_test_data</a></span><span class="op">(</span><span class="op">)</span></span></span>
 <span class="r-in"><span> <span class="va">t_df</span> <span class="op">&lt;-</span> <span class="fu">load_templates</span><span class="op">(</span><span class="fu"><a href="template_path-method.html">template_path</a></span><span class="op">(</span><span class="va">td</span><span class="op">)</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> INFO [2024-11-07 10:36:52] Reading Template_7daytreated.xlsx with load_templates_xlsx</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> INFO [2024-11-07 10:36:52] Loading Template_7daytreated.xlsx</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> INFO [2024-11-07 10:36:52] Loading Template_Untreated.xlsx</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> INFO [2024-11-07 10:36:52] Templates loaded successfully!</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> INFO [2024-12-09 10:53:18] Reading Template_7daytreated.xlsx with load_templates_xlsx</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> INFO [2024-12-09 10:53:18] Loading Template_7daytreated.xlsx</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> INFO [2024-12-09 10:53:19] Loading Template_Untreated.xlsx</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> INFO [2024-12-09 10:53:19] Templates loaded successfully!</span>
 <span class="r-in"><span></span></span>
 </code></pre></div>
     </div>
diff --git a/docs/reference/load_templates_tsv.html b/docs/reference/load_templates_tsv.html
index 0d98c79..c8c2836 100644
--- a/docs/reference/load_templates_tsv.html
+++ b/docs/reference/load_templates_tsv.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">gDRimport</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/load_templates_xlsx.html b/docs/reference/load_templates_xlsx.html
index 572b509..7bcad54 100644
--- a/docs/reference/load_templates_xlsx.html
+++ b/docs/reference/load_templates_xlsx.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">gDRimport</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/manifest_path-method.html b/docs/reference/manifest_path-method.html
index 98940b0..6b6edec 100644
--- a/docs/reference/manifest_path-method.html
+++ b/docs/reference/manifest_path-method.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">gDRimport</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/mgrepl.html b/docs/reference/mgrepl.html
index 06781ac..bc9cbf4 100644
--- a/docs/reference/mgrepl.html
+++ b/docs/reference/mgrepl.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">gDRimport</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/parse_D300_xml.html b/docs/reference/parse_D300_xml.html
index 0c2db9a..06a14a7 100644
--- a/docs/reference/parse_D300_xml.html
+++ b/docs/reference/parse_D300_xml.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">gDRimport</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/read_EnVision_delim.html b/docs/reference/read_EnVision_delim.html
index 2c909c5..d879d05 100644
--- a/docs/reference/read_EnVision_delim.html
+++ b/docs/reference/read_EnVision_delim.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">gDRimport</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/read_EnVision_xlsx.html b/docs/reference/read_EnVision_xlsx.html
index 28bc6da..32ba83d 100644
--- a/docs/reference/read_EnVision_xlsx.html
+++ b/docs/reference/read_EnVision_xlsx.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">gDRimport</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/read_excel_to_dt.html b/docs/reference/read_excel_to_dt.html
index 86b418f..2ec79fb 100644
--- a/docs/reference/read_excel_to_dt.html
+++ b/docs/reference/read_excel_to_dt.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">gDRimport</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/read_in_EnVision_file.html b/docs/reference/read_in_EnVision_file.html
index a8817d0..d31154f 100644
--- a/docs/reference/read_in_EnVision_file.html
+++ b/docs/reference/read_in_EnVision_file.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">gDRimport</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/read_in_manifest_file.html b/docs/reference/read_in_manifest_file.html
index 1bd256c..2023fa8 100644
--- a/docs/reference/read_in_manifest_file.html
+++ b/docs/reference/read_in_manifest_file.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">gDRimport</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/read_in_result_files.html b/docs/reference/read_in_result_files.html
index a09d0bb..32138a7 100644
--- a/docs/reference/read_in_result_files.html
+++ b/docs/reference/read_in_result_files.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">gDRimport</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/read_in_results_Tecan.html b/docs/reference/read_in_results_Tecan.html
index adc05d9..d520ab5 100644
--- a/docs/reference/read_in_results_Tecan.html
+++ b/docs/reference/read_in_results_Tecan.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">gDRimport</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/read_in_template_sheet_xlsx.html b/docs/reference/read_in_template_sheet_xlsx.html
index a53d264..8c28d1a 100644
--- a/docs/reference/read_in_template_sheet_xlsx.html
+++ b/docs/reference/read_in_template_sheet_xlsx.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">gDRimport</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/read_in_template_xlsx.html b/docs/reference/read_in_template_xlsx.html
index af90e92..553fe8d 100644
--- a/docs/reference/read_in_template_xlsx.html
+++ b/docs/reference/read_in_template_xlsx.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">gDRimport</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/read_in_tsv_template_files.html b/docs/reference/read_in_tsv_template_files.html
index 7865f5c..0a6231b 100644
--- a/docs/reference/read_in_tsv_template_files.html
+++ b/docs/reference/read_in_tsv_template_files.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">gDRimport</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/read_ref_data.html b/docs/reference/read_ref_data.html
index 8c79868..d9c9dc1 100644
--- a/docs/reference/read_ref_data.html
+++ b/docs/reference/read_ref_data.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">gDRimport</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/result_path-method.html b/docs/reference/result_path-method.html
index efb8c3b..0c56a3d 100644
--- a/docs/reference/result_path-method.html
+++ b/docs/reference/result_path-method.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">gDRimport</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/save_drug_info_per_well.html b/docs/reference/save_drug_info_per_well.html
index 88e8276..9badae5 100644
--- a/docs/reference/save_drug_info_per_well.html
+++ b/docs/reference/save_drug_info_per_well.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">gDRimport</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/setEnvForPSet.html b/docs/reference/setEnvForPSet.html
index 127185f..3d7e2ea 100644
--- a/docs/reference/setEnvForPSet.html
+++ b/docs/reference/setEnvForPSet.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">gDRimport</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/standardize_record_values.html b/docs/reference/standardize_record_values.html
index bdff15e..57ebba6 100644
--- a/docs/reference/standardize_record_values.html
+++ b/docs/reference/standardize_record_values.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">gDRimport</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/template_path-method.html b/docs/reference/template_path-method.html
index ca841cf..bead6c8 100644
--- a/docs/reference/template_path-method.html
+++ b/docs/reference/template_path-method.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">gDRimport</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/reference/validate_template_xlsx.html b/docs/reference/validate_template_xlsx.html
index 8892573..8e86ed7 100644
--- a/docs/reference/validate_template_xlsx.html
+++ b/docs/reference/validate_template_xlsx.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">gDRimport</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/docs/search.json b/docs/search.json
index 6b013a3..864c16c 100644
--- a/docs/search.json
+++ b/docs/search.json
@@ -1 +1 @@
-[{"path":[]},{"path":"https://gdrplatform.github.io/gDRimport/PULL_REQUEST_TEMPLATE.html","id":"what-changed","dir":"","previous_headings":"","what":"What changed?","title":"Description","text":"Related JIRA issue:","code":""},{"path":[]},{"path":"https://gdrplatform.github.io/gDRimport/PULL_REQUEST_TEMPLATE.html","id":"checklist-for-sustainable-code-base","dir":"","previous_headings":"","what":"Checklist for sustainable code base","title":"Description","text":"added tests code changed/added added documentation code changed/added made sure naming new functions self-explanatory consistent","code":""},{"path":"https://gdrplatform.github.io/gDRimport/PULL_REQUEST_TEMPLATE.html","id":"logistic-checklist","dir":"","previous_headings":"","what":"Logistic checklist","title":"Description","text":"Package version bumped Changelog updated","code":""},{"path":[]},{"path":"https://gdrplatform.github.io/gDRimport/articles/ConvertingMAEtoPharmacoSet.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"Converting a gDR-generated MultiAssayExperiment object into a PharmacoSet","text":"PharmacoGx package popular tool Bioconductor project within field bioinformatics computational biology. Whereas gDR package valuable tool provides framework import, processing, analysism visualization high-dimensional drug response data, PharmacoGx package provides functionality containerize processed drug response genomic data perform pharmacogenomic analyses. data structure used PharmacoGx described PharamcoSet class, inherited CoreGx::CoreSet. Inspired SummarizedExperiment class, new data structure class called TreatmentResponseExperiment developed store drug response data within PharmacoSet. collaboration BHKLab, developed functionality convert gDR-generated MultiAssayExperiment (MAE) object PharmacoSet object (see ConvertingPharmacoSetToGDR vignette convert PharmacoSet gDR object).","code":""},{"path":"https://gdrplatform.github.io/gDRimport/articles/ConvertingMAEtoPharmacoSet.html","id":"loading-the-gdr-generated-mae-object","dir":"Articles","previous_headings":"","what":"Loading the gDR-generated MAE object","title":"Converting a gDR-generated MultiAssayExperiment object into a PharmacoSet","text":"workflow assumes already generated MAE object using gDR package. load MAE object generated using data KW. Song et al, 2022 study. MAE contains two drugs (treatments) 7 cell lines (samples).","code":"(mae <- qs::qread(     system.file(\"extdata\", \"kyung2022mae\", \"MAE_E2.qs\", package = \"gDRimport\")   ) ) #> A MultiAssayExperiment object of 2 listed #>  experiments with user-defined names and respective classes. #>  Containing an ExperimentList class object of length 2: #>  [1] matrix: SummarizedExperiment with 1 rows and 7 columns #>  [2] single-agent: SummarizedExperiment with 2 rows and 7 columns #> Functionality: #>  experiments() - obtain the ExperimentList instance #>  colData() - the primary/phenotype DataFrame #>  sampleMap() - the sample coordination DataFrame #>  `$`, `[`, `[[` - extract colData columns, subset, or experiment #>  *Format() - convert into a long or wide DataFrame #>  assays() - convert ExperimentList to a SimpleList of matrices #>  exportClass() - save data to flat files"},{"path":"https://gdrplatform.github.io/gDRimport/articles/ConvertingMAEtoPharmacoSet.html","id":"converting-the-mae-object-into-a-pharmacoset-object","dir":"Articles","previous_headings":"","what":"Converting the MAE object into a PharmacoSet object","title":"Converting a gDR-generated MultiAssayExperiment object into a PharmacoSet","text":"First view experiments assays within MultiAssayExperiment object. now convert MAE object PharmacoSet object. need provide name data object, example use name study. can now view PharmacoSet object. can view information drugs cell lines PharmacoSet object using treatment sample slots:","code":"gDRutils::MAEpply(mae, assays) #> $matrix #> List of length 14 #> names(14): RawTreated Controls Normalized ... CIScore_50 CIScore_80 Metrics #>  #> $`single-agent` #> List of length 5 #> names(5): RawTreated Controls Normalized Averaged Metrics pset <- convert_MAE_to_PSet(mae, pset_name=\"Kyung2022\") pset #> <PharmacoSet> #> Name:  Kyung2022  #> Date Created:  Thu Nov  7 10:37:05 2024  #> Number of samples:  7  #> Molecular profiles: #>    A MultiAssayExperiment object of 1 listed #>    experiment with a user-defined name and respective class. #>    Containing an ExperimentList class object of length 1: #>    [1] emptySE: SummarizedExperiment with 0 rows and 7 columns  #> Treatment response: #>    <TreatmentResponseExperiment>  #>   dim:  3 7  #>   assays(14): RawTreated Controls Normalized Averaged SmoothMatrix BlissExcess #>     HSAExcess all_iso_points isobolograms BlissScore HSAScore CIScore_50 #>     CIScore_80 Metrics  #>   rownames(3): G02001876_Palbociclib_CDK4|CDK6_168 G02967907_GDC-0077_PI3K-A_168 G02967907_GDC-0077_PI3K-A_G02001876_Palbociclib_CDK4|CDK6_vehicle_vehicle_168  #>   rowData(10): treatmentid Gnumber DrugName ... DrugName_3 drug_moa_3 Duration  #>   colnames(7): CL129757_MCF-7_Breast_MCF-7_unknown_30 CL130218_BT-474_Breast_BT-474_unknown_70 CL130742_T-47D_Breast_T-47D_unknown_60 ... CL131873_HCC1428_Breast_HCC1428_unknown_74 CL131891_EFM-19_Breast_EFM-19_unknown_64 CL131903_BT-483_Breast_BT-483_unknown_130  #>   colData(7): sampleid clid CellLineName ... parental_identifier subtype ReferenceDivisionTime  #>   metadata(0): none head(treatmentInfo(pset)) #>                                                                     treatmentid #> 1 G02967907_GDC-0077_PI3K-A_G02001876_Palbociclib_CDK4|CDK6_vehicle_vehicle_168 #> 2                                           G02001876_Palbociclib_CDK4|CDK6_168 #> 3                                                 G02967907_GDC-0077_PI3K-A_168 #>     Gnumber    DrugName  drug_moa Gnumber_2  DrugName_2 drug_moa_2 DrugName_3 #> 1 G02967907    GDC-0077    PI3K-A G02001876 Palbociclib  CDK4|CDK6    vehicle #> 2 G02001876 Palbociclib CDK4|CDK6      <NA>        <NA>       <NA>       <NA> #> 3 G02967907    GDC-0077    PI3K-A      <NA>        <NA>       <NA>       <NA> #>   drug_moa_3 Duration #> 1    vehicle      168 #> 2       <NA>      168 #> 3       <NA>      168  head(sampleInfo(pset)) #>                                                                              sampleid #> CL129757_MCF-7_Breast_MCF-7_unknown_30         CL129757_MCF-7_Breast_MCF-7_unknown_30 #> CL130218_BT-474_Breast_BT-474_unknown_70     CL130218_BT-474_Breast_BT-474_unknown_70 #> CL130742_T-47D_Breast_T-47D_unknown_60         CL130742_T-47D_Breast_T-47D_unknown_60 #> CL131438_CAMA-1_Breast_CAMA-1_unknown_53     CL131438_CAMA-1_Breast_CAMA-1_unknown_53 #> CL131873_HCC1428_Breast_HCC1428_unknown_74 CL131873_HCC1428_Breast_HCC1428_unknown_74 #> CL131891_EFM-19_Breast_EFM-19_unknown_64     CL131891_EFM-19_Breast_EFM-19_unknown_64 #>                                                clid CellLineName Tissue #> CL129757_MCF-7_Breast_MCF-7_unknown_30     CL129757        MCF-7 Breast #> CL130218_BT-474_Breast_BT-474_unknown_70   CL130218       BT-474 Breast #> CL130742_T-47D_Breast_T-47D_unknown_60     CL130742        T-47D Breast #> CL131438_CAMA-1_Breast_CAMA-1_unknown_53   CL131438       CAMA-1 Breast #> CL131873_HCC1428_Breast_HCC1428_unknown_74 CL131873      HCC1428 Breast #> CL131891_EFM-19_Breast_EFM-19_unknown_64   CL131891       EFM-19 Breast #>                                            parental_identifier subtype #> CL129757_MCF-7_Breast_MCF-7_unknown_30                   MCF-7 unknown #> CL130218_BT-474_Breast_BT-474_unknown_70                BT-474 unknown #> CL130742_T-47D_Breast_T-47D_unknown_60                   T-47D unknown #> CL131438_CAMA-1_Breast_CAMA-1_unknown_53                CAMA-1 unknown #> CL131873_HCC1428_Breast_HCC1428_unknown_74             HCC1428 unknown #> CL131891_EFM-19_Breast_EFM-19_unknown_64                EFM-19 unknown #>                                            ReferenceDivisionTime batchid #> CL129757_MCF-7_Breast_MCF-7_unknown_30                        30       1 #> CL130218_BT-474_Breast_BT-474_unknown_70                      70       1 #> CL130742_T-47D_Breast_T-47D_unknown_60                        60       1 #> CL131438_CAMA-1_Breast_CAMA-1_unknown_53                      53       1 #> CL131873_HCC1428_Breast_HCC1428_unknown_74                    74       1 #> CL131891_EFM-19_Breast_EFM-19_unknown_64                      64       1"},{"path":"https://gdrplatform.github.io/gDRimport/articles/ConvertingMAEtoPharmacoSet.html","id":"treatmentresponseexperiment-object","dir":"Articles","previous_headings":"","what":"TreatmentResponseExperiment Object","title":"Converting a gDR-generated MultiAssayExperiment object into a PharmacoSet","text":"TreatmentResponseExperiment new class developed store drug response data within PharmacoSet object. vignette cover basics class, however information, please refer PharmacoSet vignette TreatmentResponseExperiment****.","code":""},{"path":"https://gdrplatform.github.io/gDRimport/articles/ConvertingMAEtoPharmacoSet.html","id":"row-and-column-names","dir":"Articles","previous_headings":"TreatmentResponseExperiment Object","what":"Row and Column Names","title":"Converting a gDR-generated MultiAssayExperiment object into a PharmacoSet","text":"","code":"tre <- treatmentResponse(pset) head(rownames(tre)) #> [1] \"G02001876_Palbociclib_CDK4|CDK6_168\"                                           #> [2] \"G02967907_GDC-0077_PI3K-A_168\"                                                 #> [3] \"G02967907_GDC-0077_PI3K-A_G02001876_Palbociclib_CDK4|CDK6_vehicle_vehicle_168\" head(rowData(tre)) #>                                                                      treatmentid #>                                                                           <char> #> 1:                                           G02001876_Palbociclib_CDK4|CDK6_168 #> 2:                                                 G02967907_GDC-0077_PI3K-A_168 #> 3: G02967907_GDC-0077_PI3K-A_G02001876_Palbociclib_CDK4|CDK6_vehicle_vehicle_168 #>      Gnumber    DrugName  drug_moa Gnumber_2  DrugName_2 drug_moa_2 DrugName_3 #>       <char>      <char>    <char>    <char>      <char>     <char>     <char> #> 1: G02001876 Palbociclib CDK4|CDK6      <NA>        <NA>       <NA>       <NA> #> 2: G02967907    GDC-0077    PI3K-A      <NA>        <NA>       <NA>       <NA> #> 3: G02967907    GDC-0077    PI3K-A G02001876 Palbociclib  CDK4|CDK6    vehicle #>    drug_moa_3 Duration #>        <char>    <num> #> 1:       <NA>      168 #> 2:       <NA>      168 #> 3:    vehicle      168 head(colnames(tre)) #> [1] \"CL129757_MCF-7_Breast_MCF-7_unknown_30\"     #> [2] \"CL130218_BT-474_Breast_BT-474_unknown_70\"   #> [3] \"CL130742_T-47D_Breast_T-47D_unknown_60\"     #> [4] \"CL131438_CAMA-1_Breast_CAMA-1_unknown_53\"   #> [5] \"CL131873_HCC1428_Breast_HCC1428_unknown_74\" #> [6] \"CL131891_EFM-19_Breast_EFM-19_unknown_64\" head(colData(tre)) #>                                      sampleid     clid CellLineName Tissue #>                                        <char>   <char>       <char> <char> #> 1:     CL129757_MCF-7_Breast_MCF-7_unknown_30 CL129757        MCF-7 Breast #> 2:   CL130218_BT-474_Breast_BT-474_unknown_70 CL130218       BT-474 Breast #> 3:     CL130742_T-47D_Breast_T-47D_unknown_60 CL130742        T-47D Breast #> 4:   CL131438_CAMA-1_Breast_CAMA-1_unknown_53 CL131438       CAMA-1 Breast #> 5: CL131873_HCC1428_Breast_HCC1428_unknown_74 CL131873      HCC1428 Breast #> 6:   CL131891_EFM-19_Breast_EFM-19_unknown_64 CL131891       EFM-19 Breast #>    parental_identifier subtype ReferenceDivisionTime #>                 <char>  <char>                 <num> #> 1:               MCF-7 unknown                    30 #> 2:              BT-474 unknown                    70 #> 3:               T-47D unknown                    60 #> 4:              CAMA-1 unknown                    53 #> 5:             HCC1428 unknown                    74 #> 6:              EFM-19 unknown                    64"},{"path":"https://gdrplatform.github.io/gDRimport/articles/ConvertingMAEtoPharmacoSet.html","id":"data-table-subsetting","dir":"Articles","previous_headings":"TreatmentResponseExperiment Object","what":"data.table Subsetting","title":"Converting a gDR-generated MultiAssayExperiment object into a PharmacoSet","text":"addition regex queries, TreatmentResponseExperiment object supports arbitrarily complex subset queries using data.table API. access API, need use . function, allows pass raw R expressions evaluated inside j arguments dataTable[, j]. example want subset rows cell line “CL131891_EFM-19_Breast_EFM-19_unknown_64” drug “G02967907_GDC-0077_PI3K-A_168”. can also invert matches subset columns rowData colData:","code":"tre[   .(treatmentid==\"G02967907_GDC-0077_PI3K-A_168\"), # query on row   .(sampleid==\"CL131891_EFM-19_Breast_EFM-19_unknown_64\") # query on column ] #> <TreatmentResponseExperiment>  #> dim:  1 1  #> assays(14): RawTreated Controls Normalized Averaged SmoothMatrix BlissExcess #>   HSAExcess all_iso_points isobolograms BlissScore HSAScore CIScore_50 #>   CIScore_80 Metrics  #> rownames(1): G02967907_GDC-0077_PI3K-A_168  #> rowData(10): treatmentid Gnumber DrugName ... DrugName_3 drug_moa_3 Duration  #> colnames(1): CL131891_EFM-19_Breast_EFM-19_unknown_64  #> colData(7): sampleid clid CellLineName ... parental_identifier subtype ReferenceDivisionTime  #> metadata(0): none tre[   .(treatmentid!=\"G02967907_GDC-0077_PI3K-A_168\"), # query on row   .(sampleid!=\"CL131891_EFM-19_Breast_EFM-19_unknown_64\") # query on column ] #> <TreatmentResponseExperiment>  #> dim:  2 6  #> assays(14): RawTreated Controls Normalized Averaged SmoothMatrix BlissExcess #>   HSAExcess all_iso_points isobolograms BlissScore HSAScore CIScore_50 #>   CIScore_80 Metrics  #> rownames(2): G02001876_Palbociclib_CDK4|CDK6_168 G02967907_GDC-0077_PI3K-A_G02001876_Palbociclib_CDK4|CDK6_vehicle_vehicle_168  #> rowData(10): treatmentid Gnumber DrugName ... DrugName_3 drug_moa_3 Duration  #> colnames(6): CL129757_MCF-7_Breast_MCF-7_unknown_30 CL130218_BT-474_Breast_BT-474_unknown_70 CL130742_T-47D_Breast_T-47D_unknown_60 CL131438_CAMA-1_Breast_CAMA-1_unknown_53 CL131873_HCC1428_Breast_HCC1428_unknown_74 CL131903_BT-483_Breast_BT-483_unknown_130  #> colData(7): sampleid clid CellLineName ... parental_identifier subtype ReferenceDivisionTime  #> metadata(0): none"},{"path":"https://gdrplatform.github.io/gDRimport/articles/ConvertingMAEtoPharmacoSet.html","id":"assays","dir":"Articles","previous_headings":"TreatmentResponseExperiment Object","what":"assays","title":"Converting a gDR-generated MultiAssayExperiment object into a PharmacoSet","text":"assays can viewed assays function. assay column “data_type” references SummarizedExperiment MAE data corresponds .","code":"lapply(assays(tre), head) #> $RawTreated #> Key: <treatmentid, sampleid> #>    treatmentid sampleid drug_moa drug_moa_2 drug_moa_3 DrugName DrugName_2 #>         <char>   <char>   <char>     <char>     <char>   <char>     <char> #> 1:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 2:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 3:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 4:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 5:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 6:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #>    DrugName_3 Duration Gnumber Gnumber_2 CellLineName   clid #>        <char>    <num>  <char>    <char>       <char> <char> #> 1:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 2:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 3:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 4:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 5:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 6:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #>    parental_identifier ReferenceDivisionTime subtype Tissue    data_type #>                 <char>                 <num>  <char> <char>       <char> #> 1:                <NA>                    NA    <NA>   <NA> single-agent #> 2:                <NA>                    NA    <NA>   <NA> single-agent #> 3:                <NA>                    NA    <NA>   <NA> single-agent #> 4:                <NA>                    NA    <NA>   <NA> single-agent #> 5:                <NA>                    NA    <NA>   <NA> single-agent #> 6:                <NA>                    NA    <NA>   <NA> single-agent #>    Concentration Concentration_2   Barcode ReadoutValue BackgroundValue #>            <num>           <num>    <char>        <num>           <num> #> 1:   0.001524158              NA 30190103p       921614             483 #> 2:   0.001524158              NA 30190103p       999312             483 #> 3:   0.001524158              NA 30190103p      1104556             483 #> 4:   0.001524158              NA 30190103p      1122112             483 #> 5:   0.004572471              NA 30190103p       874807             483 #> 6:   0.004572471              NA 30190103p       994797             483 #>                                Template WellRow WellColumn record_id masked #>                                  <char>  <char>     <char>     <int> <lgcl> #> 1: Template_0077_Palbo_7daytreated.xlsx       D         20      2832  FALSE #> 2: Template_0077_Palbo_7daytreated.xlsx       C         20      2831  FALSE #> 3: Template_0077_Palbo_7daytreated.xlsx       D         19      2830  FALSE #> 4: Template_0077_Palbo_7daytreated.xlsx       C         19      2829  FALSE #> 5: Template_0077_Palbo_7daytreated.xlsx       C         18      2835  FALSE #> 6: Template_0077_Palbo_7daytreated.xlsx       D         18      2836  FALSE #>    CorrectedReadout swap_sa i.Gnumber  i.DrugName i.drug_moa i.Gnumber_2 #>               <num>  <lgcl>    <char>      <char>     <char>      <char> #> 1:           921131      NA G02001876 Palbociclib  CDK4|CDK6        <NA> #> 2:           998829      NA G02001876 Palbociclib  CDK4|CDK6        <NA> #> 3:          1104073      NA G02001876 Palbociclib  CDK4|CDK6        <NA> #> 4:          1121629      NA G02001876 Palbociclib  CDK4|CDK6        <NA> #> 5:           874324      NA G02001876 Palbociclib  CDK4|CDK6        <NA> #> 6:           994314      NA G02001876 Palbociclib  CDK4|CDK6        <NA> #>    i.DrugName_2 i.drug_moa_2 i.DrugName_3 i.drug_moa_3 i.Duration   i.clid #>          <char>       <char>       <char>       <char>      <num>   <char> #> 1:         <NA>         <NA>         <NA>         <NA>        168 CL129757 #> 2:         <NA>         <NA>         <NA>         <NA>        168 CL129757 #> 3:         <NA>         <NA>         <NA>         <NA>        168 CL129757 #> 4:         <NA>         <NA>         <NA>         <NA>        168 CL129757 #> 5:         <NA>         <NA>         <NA>         <NA>        168 CL129757 #> 6:         <NA>         <NA>         <NA>         <NA>        168 CL129757 #>    i.CellLineName i.Tissue i.parental_identifier i.subtype #>            <char>   <char>                <char>    <char> #> 1:          MCF-7   Breast                 MCF-7   unknown #> 2:          MCF-7   Breast                 MCF-7   unknown #> 3:          MCF-7   Breast                 MCF-7   unknown #> 4:          MCF-7   Breast                 MCF-7   unknown #> 5:          MCF-7   Breast                 MCF-7   unknown #> 6:          MCF-7   Breast                 MCF-7   unknown #>    i.ReferenceDivisionTime #>                      <num> #> 1:                      30 #> 2:                      30 #> 3:                      30 #> 4:                      30 #> 5:                      30 #> 6:                      30 #>  #> $Controls #> Key: <treatmentid, sampleid> #>    treatmentid sampleid drug_moa drug_moa_2 drug_moa_3 DrugName DrugName_2 #>         <char>   <char>   <char>     <char>     <char>   <char>     <char> #> 1:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 2:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 3:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 4:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 5:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 6:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #>    DrugName_3 Duration Gnumber Gnumber_2 CellLineName   clid #>        <char>    <num>  <char>    <char>       <char> <char> #> 1:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 2:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 3:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 4:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 5:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 6:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #>    parental_identifier ReferenceDivisionTime subtype Tissue    data_type #>                 <char>                 <num>  <char> <char>       <char> #> 1:                <NA>                    NA    <NA>   <NA> single-agent #> 2:                <NA>                    NA    <NA>   <NA> single-agent #> 3:                <NA>                    NA    <NA>   <NA> single-agent #> 4:                <NA>                    NA    <NA>   <NA> single-agent #> 5:                <NA>                    NA    <NA>   <NA> single-agent #> 6:                <NA>                    NA    <NA>   <NA> single-agent #>    control_type CorrectedReadout record_id   Barcode isDay0 i.Gnumber #>          <char>            <num>     <int>    <char> <lgcl>    <char> #> 1:  Day0Readout            97219      2401 20190103p   TRUE G02001876 #> 2:  Day0Readout            97219      2402 20190103p   TRUE G02001876 #> 3:  Day0Readout            97219      2403 20190103p   TRUE G02001876 #> 4:  Day0Readout            97219      2404 20190103p   TRUE G02001876 #> 5:  Day0Readout            97219      2405 20190103p   TRUE G02001876 #> 6:  Day0Readout            97219      2406 20190103p   TRUE G02001876 #>     i.DrugName i.drug_moa i.Gnumber_2 i.DrugName_2 i.drug_moa_2 i.DrugName_3 #>         <char>     <char>      <char>       <char>       <char>       <char> #> 1: Palbociclib  CDK4|CDK6        <NA>         <NA>         <NA>         <NA> #> 2: Palbociclib  CDK4|CDK6        <NA>         <NA>         <NA>         <NA> #> 3: Palbociclib  CDK4|CDK6        <NA>         <NA>         <NA>         <NA> #> 4: Palbociclib  CDK4|CDK6        <NA>         <NA>         <NA>         <NA> #> 5: Palbociclib  CDK4|CDK6        <NA>         <NA>         <NA>         <NA> #> 6: Palbociclib  CDK4|CDK6        <NA>         <NA>         <NA>         <NA> #>    i.drug_moa_3 i.Duration   i.clid i.CellLineName i.Tissue #>          <char>      <num>   <char>         <char>   <char> #> 1:         <NA>        168 CL129757          MCF-7   Breast #> 2:         <NA>        168 CL129757          MCF-7   Breast #> 3:         <NA>        168 CL129757          MCF-7   Breast #> 4:         <NA>        168 CL129757          MCF-7   Breast #> 5:         <NA>        168 CL129757          MCF-7   Breast #> 6:         <NA>        168 CL129757          MCF-7   Breast #>    i.parental_identifier i.subtype i.ReferenceDivisionTime #>                   <char>    <char>                   <num> #> 1:                 MCF-7   unknown                      30 #> 2:                 MCF-7   unknown                      30 #> 3:                 MCF-7   unknown                      30 #> 4:                 MCF-7   unknown                      30 #> 5:                 MCF-7   unknown                      30 #> 6:                 MCF-7   unknown                      30 #>  #> $Normalized #> Key: <treatmentid, sampleid> #>    treatmentid sampleid drug_moa drug_moa_2 drug_moa_3 DrugName DrugName_2 #>         <char>   <char>   <char>     <char>     <char>   <char>     <char> #> 1:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 2:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 3:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 4:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 5:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 6:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #>    DrugName_3 Duration Gnumber Gnumber_2 CellLineName   clid #>        <char>    <num>  <char>    <char>       <char> <char> #> 1:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 2:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 3:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 4:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 5:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 6:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #>    parental_identifier ReferenceDivisionTime subtype Tissue    data_type #>                 <char>                 <num>  <char> <char>       <char> #> 1:                <NA>                    NA    <NA>   <NA> single-agent #> 2:                <NA>                    NA    <NA>   <NA> single-agent #> 3:                <NA>                    NA    <NA>   <NA> single-agent #> 4:                <NA>                    NA    <NA>   <NA> single-agent #> 5:                <NA>                    NA    <NA>   <NA> single-agent #> 6:                <NA>                    NA    <NA>   <NA> single-agent #>    Concentration Concentration_2 masked normalization_type      x i.Gnumber #>            <num>           <num> <lgcl>             <fctr>  <num>    <char> #> 1:   0.001524158              NA  FALSE                 RV 0.8253 G02001876 #> 2:   0.001524158              NA  FALSE                 RV 0.8949 G02001876 #> 3:   0.001524158              NA  FALSE                 RV 0.9892 G02001876 #> 4:   0.001524158              NA  FALSE                 RV 1.0049 G02001876 #> 5:   0.004572471              NA  FALSE                 RV 0.7833 G02001876 #> 6:   0.004572471              NA  FALSE                 RV 0.8908 G02001876 #>     i.DrugName i.drug_moa i.Gnumber_2 i.DrugName_2 i.drug_moa_2 i.DrugName_3 #>         <char>     <char>      <char>       <char>       <char>       <char> #> 1: Palbociclib  CDK4|CDK6        <NA>         <NA>         <NA>         <NA> #> 2: Palbociclib  CDK4|CDK6        <NA>         <NA>         <NA>         <NA> #> 3: Palbociclib  CDK4|CDK6        <NA>         <NA>         <NA>         <NA> #> 4: Palbociclib  CDK4|CDK6        <NA>         <NA>         <NA>         <NA> #> 5: Palbociclib  CDK4|CDK6        <NA>         <NA>         <NA>         <NA> #> 6: Palbociclib  CDK4|CDK6        <NA>         <NA>         <NA>         <NA> #>    i.drug_moa_3 i.Duration   i.clid i.CellLineName i.Tissue #>          <char>      <num>   <char>         <char>   <char> #> 1:         <NA>        168 CL129757          MCF-7   Breast #> 2:         <NA>        168 CL129757          MCF-7   Breast #> 3:         <NA>        168 CL129757          MCF-7   Breast #> 4:         <NA>        168 CL129757          MCF-7   Breast #> 5:         <NA>        168 CL129757          MCF-7   Breast #> 6:         <NA>        168 CL129757          MCF-7   Breast #>    i.parental_identifier i.subtype i.ReferenceDivisionTime #>                   <char>    <char>                   <num> #> 1:                 MCF-7   unknown                      30 #> 2:                 MCF-7   unknown                      30 #> 3:                 MCF-7   unknown                      30 #> 4:                 MCF-7   unknown                      30 #> 5:                 MCF-7   unknown                      30 #> 6:                 MCF-7   unknown                      30 #>  #> $Averaged #> Key: <treatmentid, sampleid> #>    treatmentid sampleid drug_moa drug_moa_2 drug_moa_3 DrugName DrugName_2 #>         <char>   <char>   <char>     <char>     <char>   <char>     <char> #> 1:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 2:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 3:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 4:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 5:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 6:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #>    DrugName_3 Duration Gnumber Gnumber_2 CellLineName   clid #>        <char>    <num>  <char>    <char>       <char> <char> #> 1:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 2:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 3:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 4:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 5:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 6:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #>    parental_identifier ReferenceDivisionTime subtype Tissue    data_type #>                 <char>                 <num>  <char> <char>       <char> #> 1:                <NA>                    NA    <NA>   <NA> single-agent #> 2:                <NA>                    NA    <NA>   <NA> single-agent #> 3:                <NA>                    NA    <NA>   <NA> single-agent #> 4:                <NA>                    NA    <NA>   <NA> single-agent #> 5:                <NA>                    NA    <NA>   <NA> single-agent #> 6:                <NA>                    NA    <NA>   <NA> single-agent #>    normalization_type Concentration Concentration_2        x      x_std #>                <fctr>         <num>           <num>    <num>      <num> #> 1:                 RV   0.001524158              NA 0.928575 0.08426274 #> 2:                 GR   0.001524158              NA 0.952225 0.05675581 #> 3:                 RV   0.004572471              NA 0.885050 0.07091133 #> 4:                 GR   0.004572471              NA 0.923000 0.04998000 #> 5:                 RV   0.013717406              NA 0.843800 0.05585201 #> 6:                 GR   0.013717406              NA 0.894475 0.04037973 #>    i.Gnumber  i.DrugName i.drug_moa i.Gnumber_2 i.DrugName_2 i.drug_moa_2 #>       <char>      <char>     <char>      <char>       <char>       <char> #> 1: G02001876 Palbociclib  CDK4|CDK6        <NA>         <NA>         <NA> #> 2: G02001876 Palbociclib  CDK4|CDK6        <NA>         <NA>         <NA> #> 3: G02001876 Palbociclib  CDK4|CDK6        <NA>         <NA>         <NA> #> 4: G02001876 Palbociclib  CDK4|CDK6        <NA>         <NA>         <NA> #> 5: G02001876 Palbociclib  CDK4|CDK6        <NA>         <NA>         <NA> #> 6: G02001876 Palbociclib  CDK4|CDK6        <NA>         <NA>         <NA> #>    i.DrugName_3 i.drug_moa_3 i.Duration   i.clid i.CellLineName i.Tissue #>          <char>       <char>      <num>   <char>         <char>   <char> #> 1:         <NA>         <NA>        168 CL129757          MCF-7   Breast #> 2:         <NA>         <NA>        168 CL129757          MCF-7   Breast #> 3:         <NA>         <NA>        168 CL129757          MCF-7   Breast #> 4:         <NA>         <NA>        168 CL129757          MCF-7   Breast #> 5:         <NA>         <NA>        168 CL129757          MCF-7   Breast #> 6:         <NA>         <NA>        168 CL129757          MCF-7   Breast #>    i.parental_identifier i.subtype i.ReferenceDivisionTime #>                   <char>    <char>                   <num> #> 1:                 MCF-7   unknown                      30 #> 2:                 MCF-7   unknown                      30 #> 3:                 MCF-7   unknown                      30 #> 4:                 MCF-7   unknown                      30 #> 5:                 MCF-7   unknown                      30 #> 6:                 MCF-7   unknown                      30 #>  #> $SmoothMatrix #> Key: <treatmentid, sampleid> #>    treatmentid sampleid drug_moa drug_moa_2 drug_moa_3 DrugName DrugName_2 #>         <char>   <char>   <char>     <char>     <char>   <char>     <char> #> 1:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 2:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 3:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 4:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 5:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 6:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #>    DrugName_3 Duration Gnumber Gnumber_2 CellLineName   clid #>        <char>    <num>  <char>    <char>       <char> <char> #> 1:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 2:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 3:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 4:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 5:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 6:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #>    parental_identifier ReferenceDivisionTime subtype Tissue    data_type #>                 <char>                 <num>  <char> <char>       <char> #> 1:                <NA>                    NA    <NA>   <NA> single-agent #> 2:                <NA>                    NA    <NA>   <NA> single-agent #> 3:                <NA>                    NA    <NA>   <NA> single-agent #> 4:                <NA>                    NA    <NA>   <NA> single-agent #> 5:                <NA>                    NA    <NA>   <NA> single-agent #> 6:                <NA>                    NA    <NA>   <NA> single-agent #>    Concentration Concentration_2     x normalization_type i.Gnumber  i.DrugName #>            <num>           <num> <num>             <char>    <char>      <char> #> 1:            NA              NA    NA               <NA> G02001876 Palbociclib #> 2:            NA              NA    NA               <NA> G02001876 Palbociclib #> 3:            NA              NA    NA               <NA> G02001876 Palbociclib #> 4:            NA              NA    NA               <NA> G02001876 Palbociclib #> 5:            NA              NA    NA               <NA> G02967907    GDC-0077 #> 6:            NA              NA    NA               <NA> G02967907    GDC-0077 #>    i.drug_moa i.Gnumber_2 i.DrugName_2 i.drug_moa_2 i.DrugName_3 i.drug_moa_3 #>        <char>      <char>       <char>       <char>       <char>       <char> #> 1:  CDK4|CDK6        <NA>         <NA>         <NA>         <NA>         <NA> #> 2:  CDK4|CDK6        <NA>         <NA>         <NA>         <NA>         <NA> #> 3:  CDK4|CDK6        <NA>         <NA>         <NA>         <NA>         <NA> #> 4:  CDK4|CDK6        <NA>         <NA>         <NA>         <NA>         <NA> #> 5:     PI3K-A        <NA>         <NA>         <NA>         <NA>         <NA> #> 6:     PI3K-A        <NA>         <NA>         <NA>         <NA>         <NA> #>    i.Duration   i.clid i.CellLineName i.Tissue i.parental_identifier i.subtype #>         <num>   <char>         <char>   <char>                <char>    <char> #> 1:        168 CL129757          MCF-7   Breast                 MCF-7   unknown #> 2:        168 CL130742          T-47D   Breast                 T-47D   unknown #> 3:        168 CL131873        HCC1428   Breast               HCC1428   unknown #> 4:        168 CL131903         BT-483   Breast                BT-483   unknown #> 5:        168 CL130218         BT-474   Breast                BT-474   unknown #> 6:        168 CL131438         CAMA-1   Breast                CAMA-1   unknown #>    i.ReferenceDivisionTime #>                      <num> #> 1:                      30 #> 2:                      60 #> 3:                      74 #> 4:                     130 #> 5:                      70 #> 6:                      53 #>  #> $BlissExcess #> Key: <treatmentid, sampleid> #>    treatmentid sampleid drug_moa drug_moa_2 drug_moa_3 DrugName DrugName_2 #>         <char>   <char>   <char>     <char>     <char>   <char>     <char> #> 1:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 2:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 3:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 4:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 5:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 6:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #>    DrugName_3 Duration Gnumber Gnumber_2 CellLineName   clid #>        <char>    <num>  <char>    <char>       <char> <char> #> 1:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 2:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 3:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 4:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 5:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 6:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #>    parental_identifier ReferenceDivisionTime subtype Tissue    data_type #>                 <char>                 <num>  <char> <char>       <char> #> 1:                <NA>                    NA    <NA>   <NA> single-agent #> 2:                <NA>                    NA    <NA>   <NA> single-agent #> 3:                <NA>                    NA    <NA>   <NA> single-agent #> 4:                <NA>                    NA    <NA>   <NA> single-agent #> 5:                <NA>                    NA    <NA>   <NA> single-agent #> 6:                <NA>                    NA    <NA>   <NA> single-agent #>    Concentration Concentration_2     x normalization_type i.Gnumber  i.DrugName #>            <num>           <num> <num>             <char>    <char>      <char> #> 1:            NA              NA    NA               <NA> G02001876 Palbociclib #> 2:            NA              NA    NA               <NA> G02001876 Palbociclib #> 3:            NA              NA    NA               <NA> G02001876 Palbociclib #> 4:            NA              NA    NA               <NA> G02001876 Palbociclib #> 5:            NA              NA    NA               <NA> G02967907    GDC-0077 #> 6:            NA              NA    NA               <NA> G02967907    GDC-0077 #>    i.drug_moa i.Gnumber_2 i.DrugName_2 i.drug_moa_2 i.DrugName_3 i.drug_moa_3 #>        <char>      <char>       <char>       <char>       <char>       <char> #> 1:  CDK4|CDK6        <NA>         <NA>         <NA>         <NA>         <NA> #> 2:  CDK4|CDK6        <NA>         <NA>         <NA>         <NA>         <NA> #> 3:  CDK4|CDK6        <NA>         <NA>         <NA>         <NA>         <NA> #> 4:  CDK4|CDK6        <NA>         <NA>         <NA>         <NA>         <NA> #> 5:     PI3K-A        <NA>         <NA>         <NA>         <NA>         <NA> #> 6:     PI3K-A        <NA>         <NA>         <NA>         <NA>         <NA> #>    i.Duration   i.clid i.CellLineName i.Tissue i.parental_identifier i.subtype #>         <num>   <char>         <char>   <char>                <char>    <char> #> 1:        168 CL129757          MCF-7   Breast                 MCF-7   unknown #> 2:        168 CL130742          T-47D   Breast                 T-47D   unknown #> 3:        168 CL131873        HCC1428   Breast               HCC1428   unknown #> 4:        168 CL131903         BT-483   Breast                BT-483   unknown #> 5:        168 CL130218         BT-474   Breast                BT-474   unknown #> 6:        168 CL131438         CAMA-1   Breast                CAMA-1   unknown #>    i.ReferenceDivisionTime #>                      <num> #> 1:                      30 #> 2:                      60 #> 3:                      74 #> 4:                     130 #> 5:                      70 #> 6:                      53 #>  #> $HSAExcess #> Key: <treatmentid, sampleid> #>    treatmentid sampleid drug_moa drug_moa_2 drug_moa_3 DrugName DrugName_2 #>         <char>   <char>   <char>     <char>     <char>   <char>     <char> #> 1:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 2:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 3:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 4:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 5:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 6:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #>    DrugName_3 Duration Gnumber Gnumber_2 CellLineName   clid #>        <char>    <num>  <char>    <char>       <char> <char> #> 1:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 2:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 3:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 4:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 5:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 6:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #>    parental_identifier ReferenceDivisionTime subtype Tissue    data_type #>                 <char>                 <num>  <char> <char>       <char> #> 1:                <NA>                    NA    <NA>   <NA> single-agent #> 2:                <NA>                    NA    <NA>   <NA> single-agent #> 3:                <NA>                    NA    <NA>   <NA> single-agent #> 4:                <NA>                    NA    <NA>   <NA> single-agent #> 5:                <NA>                    NA    <NA>   <NA> single-agent #> 6:                <NA>                    NA    <NA>   <NA> single-agent #>    Concentration Concentration_2     x normalization_type i.Gnumber  i.DrugName #>            <num>           <num> <num>             <char>    <char>      <char> #> 1:            NA              NA    NA               <NA> G02001876 Palbociclib #> 2:            NA              NA    NA               <NA> G02001876 Palbociclib #> 3:            NA              NA    NA               <NA> G02001876 Palbociclib #> 4:            NA              NA    NA               <NA> G02001876 Palbociclib #> 5:            NA              NA    NA               <NA> G02967907    GDC-0077 #> 6:            NA              NA    NA               <NA> G02967907    GDC-0077 #>    i.drug_moa i.Gnumber_2 i.DrugName_2 i.drug_moa_2 i.DrugName_3 i.drug_moa_3 #>        <char>      <char>       <char>       <char>       <char>       <char> #> 1:  CDK4|CDK6        <NA>         <NA>         <NA>         <NA>         <NA> #> 2:  CDK4|CDK6        <NA>         <NA>         <NA>         <NA>         <NA> #> 3:  CDK4|CDK6        <NA>         <NA>         <NA>         <NA>         <NA> #> 4:  CDK4|CDK6        <NA>         <NA>         <NA>         <NA>         <NA> #> 5:     PI3K-A        <NA>         <NA>         <NA>         <NA>         <NA> #> 6:     PI3K-A        <NA>         <NA>         <NA>         <NA>         <NA> #>    i.Duration   i.clid i.CellLineName i.Tissue i.parental_identifier i.subtype #>         <num>   <char>         <char>   <char>                <char>    <char> #> 1:        168 CL129757          MCF-7   Breast                 MCF-7   unknown #> 2:        168 CL130742          T-47D   Breast                 T-47D   unknown #> 3:        168 CL131873        HCC1428   Breast               HCC1428   unknown #> 4:        168 CL131903         BT-483   Breast                BT-483   unknown #> 5:        168 CL130218         BT-474   Breast                BT-474   unknown #> 6:        168 CL131438         CAMA-1   Breast                CAMA-1   unknown #>    i.ReferenceDivisionTime #>                      <num> #> 1:                      30 #> 2:                      60 #> 3:                      74 #> 4:                     130 #> 5:                      70 #> 6:                      53 #>  #> $all_iso_points #> Key: <treatmentid, sampleid> #>    treatmentid sampleid drug_moa drug_moa_2 drug_moa_3 DrugName DrugName_2 #>         <char>   <char>   <char>     <char>     <char>   <char>     <char> #> 1:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 2:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 3:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 4:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 5:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 6:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #>    DrugName_3 Duration Gnumber Gnumber_2 CellLineName   clid #>        <char>    <num>  <char>    <char>       <char> <char> #> 1:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 2:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 3:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 4:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 5:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 6:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #>    parental_identifier ReferenceDivisionTime subtype Tissue    data_type #>                 <char>                 <num>  <char> <char>       <char> #> 1:                <NA>                    NA    <NA>   <NA> single-agent #> 2:                <NA>                    NA    <NA>   <NA> single-agent #> 3:                <NA>                    NA    <NA>   <NA> single-agent #> 4:                <NA>                    NA    <NA>   <NA> single-agent #> 5:                <NA>                    NA    <NA>   <NA> single-agent #> 6:                <NA>                    NA    <NA>   <NA> single-agent #>    normalization_type i.Gnumber  i.DrugName i.drug_moa i.Gnumber_2 i.DrugName_2 #>                <char>    <char>      <char>     <char>      <char>       <char> #> 1:               <NA> G02001876 Palbociclib  CDK4|CDK6        <NA>         <NA> #> 2:               <NA> G02001876 Palbociclib  CDK4|CDK6        <NA>         <NA> #> 3:               <NA> G02001876 Palbociclib  CDK4|CDK6        <NA>         <NA> #> 4:               <NA> G02001876 Palbociclib  CDK4|CDK6        <NA>         <NA> #> 5:               <NA> G02967907    GDC-0077     PI3K-A        <NA>         <NA> #> 6:               <NA> G02967907    GDC-0077     PI3K-A        <NA>         <NA> #>    i.drug_moa_2 i.DrugName_3 i.drug_moa_3 i.Duration   i.clid i.CellLineName #>          <char>       <char>       <char>      <num>   <char>         <char> #> 1:         <NA>         <NA>         <NA>        168 CL129757          MCF-7 #> 2:         <NA>         <NA>         <NA>        168 CL130742          T-47D #> 3:         <NA>         <NA>         <NA>        168 CL131873        HCC1428 #> 4:         <NA>         <NA>         <NA>        168 CL131903         BT-483 #> 5:         <NA>         <NA>         <NA>        168 CL130218         BT-474 #> 6:         <NA>         <NA>         <NA>        168 CL131438         CAMA-1 #>    i.Tissue i.parental_identifier i.subtype i.ReferenceDivisionTime      x #>      <char>                <char>    <char>                   <num> <lgcl> #> 1:   Breast                 MCF-7   unknown                      30     NA #> 2:   Breast                 T-47D   unknown                      60     NA #> 3:   Breast               HCC1428   unknown                      74     NA #> 4:   Breast                BT-483   unknown                     130     NA #> 5:   Breast                BT-474   unknown                      70     NA #> 6:   Breast                CAMA-1   unknown                      53     NA #>  #> $isobolograms #> Key: <treatmentid, sampleid> #>    treatmentid sampleid drug_moa drug_moa_2 drug_moa_3 DrugName DrugName_2 #>         <char>   <char>   <char>     <char>     <char>   <char>     <char> #> 1:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 2:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 3:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 4:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 5:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 6:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #>    DrugName_3 Duration Gnumber Gnumber_2 CellLineName   clid #>        <char>    <num>  <char>    <char>       <char> <char> #> 1:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 2:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 3:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 4:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 5:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 6:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #>    parental_identifier ReferenceDivisionTime subtype Tissue    data_type #>                 <char>                 <num>  <char> <char>       <char> #> 1:                <NA>                    NA    <NA>   <NA> single-agent #> 2:                <NA>                    NA    <NA>   <NA> single-agent #> 3:                <NA>                    NA    <NA>   <NA> single-agent #> 4:                <NA>                    NA    <NA>   <NA> single-agent #> 5:                <NA>                    NA    <NA>   <NA> single-agent #> 6:                <NA>                    NA    <NA>   <NA> single-agent #>    normalization_type i.Gnumber  i.DrugName i.drug_moa i.Gnumber_2 i.DrugName_2 #>                <char>    <char>      <char>     <char>      <char>       <char> #> 1:               <NA> G02001876 Palbociclib  CDK4|CDK6        <NA>         <NA> #> 2:               <NA> G02001876 Palbociclib  CDK4|CDK6        <NA>         <NA> #> 3:               <NA> G02001876 Palbociclib  CDK4|CDK6        <NA>         <NA> #> 4:               <NA> G02001876 Palbociclib  CDK4|CDK6        <NA>         <NA> #> 5:               <NA> G02967907    GDC-0077     PI3K-A        <NA>         <NA> #> 6:               <NA> G02967907    GDC-0077     PI3K-A        <NA>         <NA> #>    i.drug_moa_2 i.DrugName_3 i.drug_moa_3 i.Duration   i.clid i.CellLineName #>          <char>       <char>       <char>      <num>   <char>         <char> #> 1:         <NA>         <NA>         <NA>        168 CL129757          MCF-7 #> 2:         <NA>         <NA>         <NA>        168 CL130742          T-47D #> 3:         <NA>         <NA>         <NA>        168 CL131873        HCC1428 #> 4:         <NA>         <NA>         <NA>        168 CL131903         BT-483 #> 5:         <NA>         <NA>         <NA>        168 CL130218         BT-474 #> 6:         <NA>         <NA>         <NA>        168 CL131438         CAMA-1 #>    i.Tissue i.parental_identifier i.subtype i.ReferenceDivisionTime      x #>      <char>                <char>    <char>                   <num> <lgcl> #> 1:   Breast                 MCF-7   unknown                      30     NA #> 2:   Breast                 T-47D   unknown                      60     NA #> 3:   Breast               HCC1428   unknown                      74     NA #> 4:   Breast                BT-483   unknown                     130     NA #> 5:   Breast                BT-474   unknown                      70     NA #> 6:   Breast                CAMA-1   unknown                      53     NA #>  #> $BlissScore #> Key: <treatmentid, sampleid> #>    treatmentid sampleid drug_moa drug_moa_2 drug_moa_3 DrugName DrugName_2 #>         <char>   <char>   <char>     <char>     <char>   <char>     <char> #> 1:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 2:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 3:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 4:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 5:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 6:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #>    DrugName_3 Duration Gnumber Gnumber_2 CellLineName   clid #>        <char>    <num>  <char>    <char>       <char> <char> #> 1:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 2:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 3:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 4:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 5:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 6:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #>    parental_identifier ReferenceDivisionTime subtype Tissue    data_type #>                 <char>                 <num>  <char> <char>       <char> #> 1:                <NA>                    NA    <NA>   <NA> single-agent #> 2:                <NA>                    NA    <NA>   <NA> single-agent #> 3:                <NA>                    NA    <NA>   <NA> single-agent #> 4:                <NA>                    NA    <NA>   <NA> single-agent #> 5:                <NA>                    NA    <NA>   <NA> single-agent #> 6:                <NA>                    NA    <NA>   <NA> single-agent #>    normalization_type     x i.Gnumber  i.DrugName i.drug_moa i.Gnumber_2 #>                <char> <num>    <char>      <char>     <char>      <char> #> 1:               <NA>    NA G02001876 Palbociclib  CDK4|CDK6        <NA> #> 2:               <NA>    NA G02001876 Palbociclib  CDK4|CDK6        <NA> #> 3:               <NA>    NA G02001876 Palbociclib  CDK4|CDK6        <NA> #> 4:               <NA>    NA G02001876 Palbociclib  CDK4|CDK6        <NA> #> 5:               <NA>    NA G02967907    GDC-0077     PI3K-A        <NA> #> 6:               <NA>    NA G02967907    GDC-0077     PI3K-A        <NA> #>    i.DrugName_2 i.drug_moa_2 i.DrugName_3 i.drug_moa_3 i.Duration   i.clid #>          <char>       <char>       <char>       <char>      <num>   <char> #> 1:         <NA>         <NA>         <NA>         <NA>        168 CL129757 #> 2:         <NA>         <NA>         <NA>         <NA>        168 CL130742 #> 3:         <NA>         <NA>         <NA>         <NA>        168 CL131873 #> 4:         <NA>         <NA>         <NA>         <NA>        168 CL131903 #> 5:         <NA>         <NA>         <NA>         <NA>        168 CL130218 #> 6:         <NA>         <NA>         <NA>         <NA>        168 CL131438 #>    i.CellLineName i.Tissue i.parental_identifier i.subtype #>            <char>   <char>                <char>    <char> #> 1:          MCF-7   Breast                 MCF-7   unknown #> 2:          T-47D   Breast                 T-47D   unknown #> 3:        HCC1428   Breast               HCC1428   unknown #> 4:         BT-483   Breast                BT-483   unknown #> 5:         BT-474   Breast                BT-474   unknown #> 6:         CAMA-1   Breast                CAMA-1   unknown #>    i.ReferenceDivisionTime #>                      <num> #> 1:                      30 #> 2:                      60 #> 3:                      74 #> 4:                     130 #> 5:                      70 #> 6:                      53 #>  #> $HSAScore #> Key: <treatmentid, sampleid> #>    treatmentid sampleid drug_moa drug_moa_2 drug_moa_3 DrugName DrugName_2 #>         <char>   <char>   <char>     <char>     <char>   <char>     <char> #> 1:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 2:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 3:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 4:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 5:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 6:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #>    DrugName_3 Duration Gnumber Gnumber_2 CellLineName   clid #>        <char>    <num>  <char>    <char>       <char> <char> #> 1:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 2:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 3:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 4:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 5:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 6:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #>    parental_identifier ReferenceDivisionTime subtype Tissue    data_type #>                 <char>                 <num>  <char> <char>       <char> #> 1:                <NA>                    NA    <NA>   <NA> single-agent #> 2:                <NA>                    NA    <NA>   <NA> single-agent #> 3:                <NA>                    NA    <NA>   <NA> single-agent #> 4:                <NA>                    NA    <NA>   <NA> single-agent #> 5:                <NA>                    NA    <NA>   <NA> single-agent #> 6:                <NA>                    NA    <NA>   <NA> single-agent #>    normalization_type     x i.Gnumber  i.DrugName i.drug_moa i.Gnumber_2 #>                <char> <num>    <char>      <char>     <char>      <char> #> 1:               <NA>    NA G02001876 Palbociclib  CDK4|CDK6        <NA> #> 2:               <NA>    NA G02001876 Palbociclib  CDK4|CDK6        <NA> #> 3:               <NA>    NA G02001876 Palbociclib  CDK4|CDK6        <NA> #> 4:               <NA>    NA G02001876 Palbociclib  CDK4|CDK6        <NA> #> 5:               <NA>    NA G02967907    GDC-0077     PI3K-A        <NA> #> 6:               <NA>    NA G02967907    GDC-0077     PI3K-A        <NA> #>    i.DrugName_2 i.drug_moa_2 i.DrugName_3 i.drug_moa_3 i.Duration   i.clid #>          <char>       <char>       <char>       <char>      <num>   <char> #> 1:         <NA>         <NA>         <NA>         <NA>        168 CL129757 #> 2:         <NA>         <NA>         <NA>         <NA>        168 CL130742 #> 3:         <NA>         <NA>         <NA>         <NA>        168 CL131873 #> 4:         <NA>         <NA>         <NA>         <NA>        168 CL131903 #> 5:         <NA>         <NA>         <NA>         <NA>        168 CL130218 #> 6:         <NA>         <NA>         <NA>         <NA>        168 CL131438 #>    i.CellLineName i.Tissue i.parental_identifier i.subtype #>            <char>   <char>                <char>    <char> #> 1:          MCF-7   Breast                 MCF-7   unknown #> 2:          T-47D   Breast                 T-47D   unknown #> 3:        HCC1428   Breast               HCC1428   unknown #> 4:         BT-483   Breast                BT-483   unknown #> 5:         BT-474   Breast                BT-474   unknown #> 6:         CAMA-1   Breast                CAMA-1   unknown #>    i.ReferenceDivisionTime #>                      <num> #> 1:                      30 #> 2:                      60 #> 3:                      74 #> 4:                     130 #> 5:                      70 #> 6:                      53 #>  #> $CIScore_50 #> Key: <treatmentid, sampleid> #>    treatmentid sampleid drug_moa drug_moa_2 drug_moa_3 DrugName DrugName_2 #>         <char>   <char>   <char>     <char>     <char>   <char>     <char> #> 1:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 2:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 3:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 4:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 5:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 6:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #>    DrugName_3 Duration Gnumber Gnumber_2 CellLineName   clid #>        <char>    <num>  <char>    <char>       <char> <char> #> 1:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 2:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 3:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 4:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 5:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 6:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #>    parental_identifier ReferenceDivisionTime subtype Tissue    data_type #>                 <char>                 <num>  <char> <char>       <char> #> 1:                <NA>                    NA    <NA>   <NA> single-agent #> 2:                <NA>                    NA    <NA>   <NA> single-agent #> 3:                <NA>                    NA    <NA>   <NA> single-agent #> 4:                <NA>                    NA    <NA>   <NA> single-agent #> 5:                <NA>                    NA    <NA>   <NA> single-agent #> 6:                <NA>                    NA    <NA>   <NA> single-agent #>    normalization_type      x i.Gnumber  i.DrugName i.drug_moa i.Gnumber_2 #>                <char> <lgcl>    <char>      <char>     <char>      <char> #> 1:               <NA>     NA G02001876 Palbociclib  CDK4|CDK6        <NA> #> 2:               <NA>     NA G02001876 Palbociclib  CDK4|CDK6        <NA> #> 3:               <NA>     NA G02001876 Palbociclib  CDK4|CDK6        <NA> #> 4:               <NA>     NA G02001876 Palbociclib  CDK4|CDK6        <NA> #> 5:               <NA>     NA G02967907    GDC-0077     PI3K-A        <NA> #> 6:               <NA>     NA G02967907    GDC-0077     PI3K-A        <NA> #>    i.DrugName_2 i.drug_moa_2 i.DrugName_3 i.drug_moa_3 i.Duration   i.clid #>          <char>       <char>       <char>       <char>      <num>   <char> #> 1:         <NA>         <NA>         <NA>         <NA>        168 CL129757 #> 2:         <NA>         <NA>         <NA>         <NA>        168 CL130742 #> 3:         <NA>         <NA>         <NA>         <NA>        168 CL131873 #> 4:         <NA>         <NA>         <NA>         <NA>        168 CL131903 #> 5:         <NA>         <NA>         <NA>         <NA>        168 CL130218 #> 6:         <NA>         <NA>         <NA>         <NA>        168 CL131438 #>    i.CellLineName i.Tissue i.parental_identifier i.subtype #>            <char>   <char>                <char>    <char> #> 1:          MCF-7   Breast                 MCF-7   unknown #> 2:          T-47D   Breast                 T-47D   unknown #> 3:        HCC1428   Breast               HCC1428   unknown #> 4:         BT-483   Breast                BT-483   unknown #> 5:         BT-474   Breast                BT-474   unknown #> 6:         CAMA-1   Breast                CAMA-1   unknown #>    i.ReferenceDivisionTime #>                      <num> #> 1:                      30 #> 2:                      60 #> 3:                      74 #> 4:                     130 #> 5:                      70 #> 6:                      53 #>  #> $CIScore_80 #> Key: <treatmentid, sampleid> #>    treatmentid sampleid drug_moa drug_moa_2 drug_moa_3 DrugName DrugName_2 #>         <char>   <char>   <char>     <char>     <char>   <char>     <char> #> 1:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 2:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 3:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 4:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 5:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 6:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #>    DrugName_3 Duration Gnumber Gnumber_2 CellLineName   clid #>        <char>    <num>  <char>    <char>       <char> <char> #> 1:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 2:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 3:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 4:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 5:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 6:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #>    parental_identifier ReferenceDivisionTime subtype Tissue    data_type #>                 <char>                 <num>  <char> <char>       <char> #> 1:                <NA>                    NA    <NA>   <NA> single-agent #> 2:                <NA>                    NA    <NA>   <NA> single-agent #> 3:                <NA>                    NA    <NA>   <NA> single-agent #> 4:                <NA>                    NA    <NA>   <NA> single-agent #> 5:                <NA>                    NA    <NA>   <NA> single-agent #> 6:                <NA>                    NA    <NA>   <NA> single-agent #>    normalization_type      x i.Gnumber  i.DrugName i.drug_moa i.Gnumber_2 #>                <char> <lgcl>    <char>      <char>     <char>      <char> #> 1:               <NA>     NA G02001876 Palbociclib  CDK4|CDK6        <NA> #> 2:               <NA>     NA G02001876 Palbociclib  CDK4|CDK6        <NA> #> 3:               <NA>     NA G02001876 Palbociclib  CDK4|CDK6        <NA> #> 4:               <NA>     NA G02001876 Palbociclib  CDK4|CDK6        <NA> #> 5:               <NA>     NA G02967907    GDC-0077     PI3K-A        <NA> #> 6:               <NA>     NA G02967907    GDC-0077     PI3K-A        <NA> #>    i.DrugName_2 i.drug_moa_2 i.DrugName_3 i.drug_moa_3 i.Duration   i.clid #>          <char>       <char>       <char>       <char>      <num>   <char> #> 1:         <NA>         <NA>         <NA>         <NA>        168 CL129757 #> 2:         <NA>         <NA>         <NA>         <NA>        168 CL130742 #> 3:         <NA>         <NA>         <NA>         <NA>        168 CL131873 #> 4:         <NA>         <NA>         <NA>         <NA>        168 CL131903 #> 5:         <NA>         <NA>         <NA>         <NA>        168 CL130218 #> 6:         <NA>         <NA>         <NA>         <NA>        168 CL131438 #>    i.CellLineName i.Tissue i.parental_identifier i.subtype #>            <char>   <char>                <char>    <char> #> 1:          MCF-7   Breast                 MCF-7   unknown #> 2:          T-47D   Breast                 T-47D   unknown #> 3:        HCC1428   Breast               HCC1428   unknown #> 4:         BT-483   Breast                BT-483   unknown #> 5:         BT-474   Breast                BT-474   unknown #> 6:         CAMA-1   Breast                CAMA-1   unknown #>    i.ReferenceDivisionTime #>                      <num> #> 1:                      30 #> 2:                      60 #> 3:                      74 #> 4:                     130 #> 5:                      70 #> 6:                      53 #>  #> $Metrics #> Key: <treatmentid, sampleid> #>    treatmentid sampleid drug_moa drug_moa_2 drug_moa_3 DrugName DrugName_2 #>         <char>   <char>   <char>     <char>     <char>   <char>     <char> #> 1:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 2:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 3:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 4:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 5:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 6:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #>    DrugName_3 Duration Gnumber Gnumber_2 CellLineName   clid #>        <char>    <num>  <char>    <char>       <char> <char> #> 1:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 2:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 3:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 4:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 5:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 6:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #>    parental_identifier ReferenceDivisionTime subtype Tissue    data_type #>                 <char>                 <num>  <char> <char>       <char> #> 1:                <NA>                    NA    <NA>   <NA> single-agent #> 2:                <NA>                    NA    <NA>   <NA> single-agent #> 3:                <NA>                    NA    <NA>   <NA> single-agent #> 4:                <NA>                    NA    <NA>   <NA> single-agent #> 5:                <NA>                    NA    <NA>   <NA> single-agent #> 6:                <NA>                    NA    <NA>   <NA> single-agent #>       x_mean     x_AOC x_AOC_range       xc50    x_max       ec50      x_inf #>        <num>     <num>       <num>      <num>    <num>      <num>      <num> #> 1: 0.4766169 0.5233831   0.5685724 0.07649828 0.107050 0.06354470 0.08684205 #> 2: 0.6438030 0.3561970   0.3828886 0.26119890 0.281750 0.09897928 0.32080324 #> 3: 0.5797408 0.4202592   0.4560827 0.10802210 0.207125 0.08784832 0.21933259 #> 4: 0.4888085 0.5111915   0.5620006 0.06629065 0.111625 0.05911087 0.12311310 #> 5: 0.6458536 0.3541464   0.3770687 0.26781723 0.228300 0.13626047 0.27577126 #> 6: 0.4821213 0.5178787   0.5639825 0.06294109 0.148225 0.04029515 0.16592442 #>      x_0         h        r2   x_sd_avg               fit_type #>    <num>     <num>     <num>      <num>                 <char> #> 1:     1 1.0283168 0.9853800 0.05272629 DRC3pHillFitModelFixS0 #> 2:     1 1.0574543 0.9465590 0.07259453 DRC3pHillFitModelFixS0 #> 3:     1 2.7932767 0.9787945 0.06655135 DRC3pHillFitModelFixS0 #> 4:     1 2.4657832 0.9946671 0.07915584 DRC3pHillFitModelFixS0 #> 5:     1 1.1867664 0.9616801 0.06463053 DRC3pHillFitModelFixS0 #> 6:     1 0.9041923 0.9740112 0.05594059 DRC3pHillFitModelFixS0 #>    maxlog10Concentration N_conc normalization_type fit_source cotrt_value #>                    <num>  <int>             <char>     <char>       <num> #> 1:                     1     10                 RV        gDR          NA #> 2:                     1     10                 RV        gDR          NA #> 3:                     1     10                 RV        gDR          NA #> 4:                     1     10                 RV        gDR          NA #> 5:                     1     10                 RV        gDR          NA #> 6:                     1     10                 RV        gDR          NA #>    source i.Gnumber  i.DrugName i.drug_moa i.Gnumber_2 i.DrugName_2 #>    <char>    <char>      <char>     <char>      <char>       <char> #> 1:   <NA> G02001876 Palbociclib  CDK4|CDK6        <NA>         <NA> #> 2:   <NA> G02001876 Palbociclib  CDK4|CDK6        <NA>         <NA> #> 3:   <NA> G02001876 Palbociclib  CDK4|CDK6        <NA>         <NA> #> 4:   <NA> G02001876 Palbociclib  CDK4|CDK6        <NA>         <NA> #> 5:   <NA> G02001876 Palbociclib  CDK4|CDK6        <NA>         <NA> #> 6:   <NA> G02001876 Palbociclib  CDK4|CDK6        <NA>         <NA> #>    i.drug_moa_2 i.DrugName_3 i.drug_moa_3 i.Duration   i.clid i.CellLineName #>          <char>       <char>       <char>      <num>   <char>         <char> #> 1:         <NA>         <NA>         <NA>        168 CL129757          MCF-7 #> 2:         <NA>         <NA>         <NA>        168 CL130218         BT-474 #> 3:         <NA>         <NA>         <NA>        168 CL130742          T-47D #> 4:         <NA>         <NA>         <NA>        168 CL131438         CAMA-1 #> 5:         <NA>         <NA>         <NA>        168 CL131873        HCC1428 #> 6:         <NA>         <NA>         <NA>        168 CL131891         EFM-19 #>    i.Tissue i.parental_identifier i.subtype i.ReferenceDivisionTime #>      <char>                <char>    <char>                   <num> #> 1:   Breast                 MCF-7   unknown                      30 #> 2:   Breast                BT-474   unknown                      70 #> 3:   Breast                 T-47D   unknown                      60 #> 4:   Breast                CAMA-1   unknown                      53 #> 5:   Breast               HCC1428   unknown                      74 #> 6:   Breast                EFM-19   unknown                      64 assayNames(tre) #>  [1] \"RawTreated\"     \"Controls\"       \"Normalized\"     \"Averaged\"       #>  [5] \"SmoothMatrix\"   \"BlissExcess\"    \"HSAExcess\"      \"all_iso_points\" #>  [9] \"isobolograms\"   \"BlissScore\"     \"HSAScore\"       \"CIScore_50\"     #> [13] \"CIScore_80\"     \"Metrics\" head(assay(tre, \"Metrics\"),3) #> Key: <treatmentid, sampleid> #>                            treatmentid                                 sampleid #>                                 <char>                                   <char> #> 1: G02001876_Palbociclib_CDK4|CDK6_168   CL129757_MCF-7_Breast_MCF-7_unknown_30 #> 2: G02001876_Palbociclib_CDK4|CDK6_168 CL130218_BT-474_Breast_BT-474_unknown_70 #> 3: G02001876_Palbociclib_CDK4|CDK6_168   CL130742_T-47D_Breast_T-47D_unknown_60 #>     drug_moa drug_moa_2 drug_moa_3    DrugName DrugName_2 DrugName_3 Duration #>       <char>     <char>     <char>      <char>     <char>     <char>    <num> #> 1: CDK4|CDK6       <NA>       <NA> Palbociclib       <NA>       <NA>      168 #> 2: CDK4|CDK6       <NA>       <NA> Palbociclib       <NA>       <NA>      168 #> 3: CDK4|CDK6       <NA>       <NA> Palbociclib       <NA>       <NA>      168 #>      Gnumber Gnumber_2 CellLineName     clid parental_identifier #>       <char>    <char>       <char>   <char>              <char> #> 1: G02001876      <NA>        MCF-7 CL129757               MCF-7 #> 2: G02001876      <NA>       BT-474 CL130218              BT-474 #> 3: G02001876      <NA>        T-47D CL130742               T-47D #>    ReferenceDivisionTime subtype Tissue    data_type    x_mean     x_AOC #>                    <num>  <char> <char>       <char>     <num>     <num> #> 1:                    30 unknown Breast single-agent 0.4774514 0.5225486 #> 2:                    70 unknown Breast single-agent 0.5916887 0.4083113 #> 3:                    60 unknown Breast single-agent 0.5478704 0.4521296 #>    x_AOC_range      xc50     x_max      ec50       x_inf   x_0         h #>          <num>     <num>     <num>     <num>       <num> <num>     <num> #> 1:   0.5592516 0.1100133 -0.017025 0.1161741 -0.03117468     1 1.1100114 #> 2:   0.4338082 0.2091202  0.114275 0.1360264  0.16571556     1 0.9361851 #> 3:   0.4876840 0.1164343  0.111425 0.1033672  0.13053185     1 2.5415386 #>           r2   x_sd_avg               fit_type maxlog10Concentration N_conc #>        <num>      <num>                 <char>                 <num>  <int> #> 1: 0.9880388 0.05887778 DRC3pHillFitModelFixS0                     1     10 #> 2: 0.9555750 0.08197778 DRC3pHillFitModelFixS0                     1     10 #> 3: 0.9815621 0.06581980 DRC3pHillFitModelFixS0                     1     10 #>    normalization_type fit_source cotrt_value source i.Gnumber  i.DrugName #>                <char>     <char>       <num> <char>    <char>      <char> #> 1:                 GR        gDR          NA   <NA> G02001876 Palbociclib #> 2:                 GR        gDR          NA   <NA> G02001876 Palbociclib #> 3:                 GR        gDR          NA   <NA> G02001876 Palbociclib #>    i.drug_moa i.Gnumber_2 i.DrugName_2 i.drug_moa_2 i.DrugName_3 i.drug_moa_3 #>        <char>      <char>       <char>       <char>       <char>       <char> #> 1:  CDK4|CDK6        <NA>         <NA>         <NA>         <NA>         <NA> #> 2:  CDK4|CDK6        <NA>         <NA>         <NA>         <NA>         <NA> #> 3:  CDK4|CDK6        <NA>         <NA>         <NA>         <NA>         <NA> #>    i.Duration   i.clid i.CellLineName i.Tissue i.parental_identifier i.subtype #>         <num>   <char>         <char>   <char>                <char>    <char> #> 1:        168 CL129757          MCF-7   Breast                 MCF-7   unknown #> 2:        168 CL130218         BT-474   Breast                BT-474   unknown #> 3:        168 CL130742          T-47D   Breast                 T-47D   unknown #>    i.ReferenceDivisionTime #>                      <num> #> 1:                      30 #> 2:                      70 #> 3:                      60"},{"path":"https://gdrplatform.github.io/gDRimport/articles/ConvertingMAEtoPharmacoSet.html","id":"references","dir":"Articles","previous_headings":"","what":"References","title":"Converting a gDR-generated MultiAssayExperiment object into a PharmacoSet","text":"Song, K. W., Edgar, K. ., Hanan, E. J., Hafner, M., Oeh, J., Merchant, M., … & Friedman, L. S. (2022). RTK-dependent inducible degradation mutant PI3K drives GDC-0077 (Inavolisib) efficacy. Cancer discovery, 12(1), 204-219.","code":"sessionInfo() #> R version 4.3.0 (2023-04-21) #> Platform: x86_64-pc-linux-gnu (64-bit) #> Running under: Ubuntu 22.04.3 LTS #>  #> Matrix products: default #> BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3  #> LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;  LAPACK version 3.10.0 #>  #> locale: #>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               #>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     #>  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8    #>  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  #>  [9] LC_ADDRESS=C               LC_TELEPHONE=C             #> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C        #>  #> time zone: Etc/UTC #> tzcode source: system (glibc) #>  #> attached base packages: #> [1] stats4    stats     graphics  grDevices utils     datasets  methods   #> [8] base      #>  #> other attached packages: #>  [1] MultiAssayExperiment_1.28.0 gDRimport_1.5.2             #>  [3] PharmacoGx_3.6.0            CoreGx_2.6.1                #>  [5] SummarizedExperiment_1.32.0 Biobase_2.62.0              #>  [7] GenomicRanges_1.54.1        GenomeInfoDb_1.38.8         #>  [9] IRanges_2.36.0              S4Vectors_0.40.2            #> [11] MatrixGenerics_1.14.0       matrixStats_1.4.1           #> [13] BiocGenerics_0.48.1         #>  #> loaded via a namespace (and not attached): #>   [1] bitops_1.0-9            rlang_1.1.4             magrittr_2.0.3          #>   [4] shinydashboard_0.7.2    compiler_4.3.0          reshape2_1.4.4          #>   [7] maps_3.4.2              systemfonts_1.0.5       vctrs_0.6.5             #>  [10] relations_0.6-13        stringr_1.5.1           pkgconfig_2.0.3         #>  [13] crayon_1.5.3            fastmap_1.2.0           backports_1.5.0         #>  [16] XVector_0.42.0          caTools_1.18.3          utf8_1.2.4              #>  [19] promises_1.3.0          rmarkdown_2.29          pracma_2.4.4            #>  [22] ragg_1.2.7              magicaxis_2.4.5         coop_0.6-3              #>  [25] purrr_1.0.2             xfun_0.49               zlibbioc_1.48.2         #>  [28] cachem_1.1.0            celestial_1.4.6         jsonlite_1.8.9          #>  [31] SnowballC_0.7.1         later_1.3.2             DelayedArray_0.28.0     #>  [34] BiocParallel_1.36.0     parallel_4.3.0          sets_1.0-25             #>  [37] cluster_2.1.4           R6_2.5.1                stringi_1.8.4           #>  [40] bslib_0.8.0             RColorBrewer_1.1-3      qs_0.27.2               #>  [43] limma_3.58.1            boot_1.3-28.1           jquerylib_0.1.4         #>  [46] Rcpp_1.0.13-1           knitr_1.48              downloader_0.4          #>  [49] httpuv_1.6.15           Matrix_1.6-5            igraph_2.1.1            #>  [52] tidyselect_1.2.1        abind_1.4-8             yaml_2.3.10             #>  [55] stringfish_0.16.0       gplots_3.2.0            codetools_0.2-19        #>  [58] plyr_1.8.9              lattice_0.21-8          tibble_3.2.1            #>  [61] shiny_1.9.1             BumpyMatrix_1.10.0      evaluate_1.0.1          #>  [64] desc_1.4.3              RcppParallel_5.1.7      bench_1.1.3             #>  [67] pillar_1.9.0            lsa_0.73.3              KernSmooth_2.23-20      #>  [70] sm_2.2-6.0              checkmate_2.3.2         DT_0.33                 #>  [73] shinyjs_2.1.0           piano_2.18.0            generics_0.1.3          #>  [76] RCurl_1.98-1.16         ggplot2_3.5.1           munsell_0.5.1           #>  [79] scales_1.3.0            RApiSerialize_0.1.4     gtools_3.9.5            #>  [82] xtable_1.8-4            marray_1.80.0           glue_1.8.0              #>  [85] slam_0.1-54             mapproj_1.2.11          tools_4.3.0             #>  [88] data.table_1.16.2       gDRutils_1.5.2          fgsea_1.28.0            #>  [91] RANN_2.6.2              fs_1.6.5                visNetwork_2.1.2        #>  [94] fastmatch_1.1-4         cowplot_1.1.3           grid_4.3.0              #>  [97] plotrix_3.8-4           NISTunits_1.0.1         colorspace_2.1-1        #> [100] GenomeInfoDbData_1.2.11 cli_3.6.3               textshaping_0.3.7       #> [103] fansi_1.0.6             S4Arrays_1.2.1          dplyr_1.1.4             #> [106] gtable_0.3.6            sass_0.4.9              digest_0.6.37           #> [109] SparseArray_1.2.4       htmlwidgets_1.6.4       memoise_2.0.1           #> [112] htmltools_0.5.8.1       pkgdown_2.0.7           lifecycle_1.0.4         #> [115] statmod_1.5.0           mime_0.12               MASS_7.3-58.4"},{"path":"https://gdrplatform.github.io/gDRimport/articles/ConvertingPharmacoSetToGDR.html","id":"overview","dir":"Articles","previous_headings":"","what":"Overview","title":"Converting PharmacoSet Drug Response Data into gDR object","text":"gDRimport package part gDR suite. helps prepare raw drug response data downstream processing. mainly contains helper functions importing/loading/validating dose response data provided different scanner sources. collaboration BHKLab, gDRimport also provides functions can convert PharmacoGx::PharamcoSet object gDR object. functionality, users familiar gDR suite packages methods can utilize publically available, curated datasets PharmacoGx database. main step process extract drug dose-response data PharmacoSets transform data.table can used input gDRcore::runDrugResponseProcessingPipeline.","code":""},{"path":"https://gdrplatform.github.io/gDRimport/articles/ConvertingPharmacoSetToGDR.html","id":"loading-a-pharmacoset-pset","dir":"Articles","previous_headings":"","what":"Loading a PharmacoSet (PSet)","title":"Converting PharmacoSet Drug Response Data into gDR object","text":"Whereas user might already pharmacoset loaded R session, wish obtain different pharmacoset use script future provide helper function . helps user directory store pharmacosets, passing directory function parameter, function also check see PSet exists user-defined directory. ensure PSet re-downloaded already .","code":"pset <- getPSet(\"Tavor_2020\") pset"},{"path":"https://gdrplatform.github.io/gDRimport/articles/ConvertingPharmacoSetToGDR.html","id":"converting-pharmacoset-to-data-table-for-gdr-pipeline","dir":"Articles","previous_headings":"","what":"Converting PharmacoSet to data.table for gDR pipeline","title":"Converting PharmacoSet Drug Response Data into gDR object","text":"PharamcoSets hold data pertaining cell lines (@sample slot), drugs (@treatment slot), dose response experiments (@treatmentResponse slot). dose response data stored treatmentResponseExperiment object function gDRimport::convert_pset_to_df extracts information build data.table can used input gDR pipeline.","code":"# Store treatment response data in df_  dt <- convert_pset_to_df(pharmacoset = pset) str(dt) #> Classes 'data.table' and 'data.frame':   34516 obs. of  7 variables: #>  $ Barcode              : chr  \"PCM-0103090_1_130695_2018-08-28\" \"PCM-0103090_1_130695_2018-08-28\" \"PCM-0103090_1_130695_2018-08-28\" \"PCM-0103090_1_130695_2018-08-28\" ... #>  $ ReadoutValue         : num  75.7 63.1 75.9 87.2 78.8 ... #>  $ Concentration        : num  0.0021 0.0052 0.01 0.0299 0.0798 ... #>  $ Clid                 : chr  \"130695\" \"130695\" \"130695\" \"130695\" ... #>  $ DrugName             : chr  \"Ivosidenib\" \"Ivosidenib\" \"Ivosidenib\" \"Ivosidenib\" ... #>  $ Duration             : num  48 48 48 48 48 48 48 48 48 48 ... #>  $ ReferenceDivisionTime: logi  NA NA NA NA NA NA ... #>  - attr(*, \".internal.selfref\")=<externalptr>"},{"path":"https://gdrplatform.github.io/gDRimport/articles/ConvertingPharmacoSetToGDR.html","id":"subsetting-to-extract-relevant-information","dir":"Articles","previous_headings":"","what":"Subsetting to extract relevant information","title":"Converting PharmacoSet Drug Response Data into gDR object","text":"canonical PharmacoSets data pertaining many cell lines response many drugs (drug-combination data available conversion gDR currently supported). , interest time resources, may useful subset data providing input gDR pipeline.","code":"# example subset using only 1 cell line subset_cl <- dt$Clid[1] x <- dt[Clid == subset_cl] x #>                              Barcode ReadoutValue Concentration   Clid #>                               <char>        <num>         <num> <char> #>   1: PCM-0103090_1_130695_2018-08-28       75.733        0.0021 130695 #>   2: PCM-0103090_1_130695_2018-08-28       63.094        0.0052 130695 #>   3: PCM-0103090_1_130695_2018-08-28       75.935        0.0100 130695 #>   4: PCM-0103090_1_130695_2018-08-28       87.159        0.0299 130695 #>   5: PCM-0103090_1_130695_2018-08-28       78.766        0.0798 130695 #>  ---                                                                   #> 589: PCM-0064526_5_130695_2018-08-28       71.707        1.4960 130695 #> 590: PCM-0064526_5_130695_2018-08-28       60.488        3.9900 130695 #> 591: PCM-0064526_5_130695_2018-08-28       25.366        9.9750 130695 #> 592: PCM-0064526_5_130695_2018-08-28        5.976       24.9400 130695 #> 593: PCM-0064526_5_130695_2018-08-28      100.000        0.0000 130695 #>         DrugName Duration ReferenceDivisionTime #>           <char>    <num>                <lgcl> #>   1:  Ivosidenib       48                    NA #>   2:  Ivosidenib       48                    NA #>   3:  Ivosidenib       48                    NA #>   4:  Ivosidenib       48                    NA #>   5:  Ivosidenib       48                    NA #>  ---                                            #> 589: Azacitidine       48                    NA #> 590: Azacitidine       48                    NA #> 591: Azacitidine       48                    NA #> 592: Azacitidine       48                    NA #> 593:     vehicle       48                    NA"},{"path":"https://gdrplatform.github.io/gDRimport/articles/ConvertingPharmacoSetToGDR.html","id":"running-drug-response-pipeline-with-data","dir":"Articles","previous_headings":"","what":"Running drug response pipeline with data","title":"Converting PharmacoSet Drug Response Data into gDR object","text":"subsetted data can now used input gDRcore::runDrugResponseProcessingPipeline(). output function MultiAssayExperiment object can accessed gDRutils::convert_se_assay_to_dt()","code":"# RUN DRUG RESPONSE PROCESSING PIPELINE se <- gDRcore::runDrugResponseProcessingPipeline(x) se # Convert Summarized Experiments to data.table  # Available SEs : \"RawTreatred\", \"Controls\", \"Normalized\", \"Averaged\", \"Metrics\"  str(gDRutils::convert_se_assay_to_dt(se[[1]], \"Averaged\")) str(gDRutils::convert_se_assay_to_dt(se[[1]], \"Metrics\"))"},{"path":"https://gdrplatform.github.io/gDRimport/articles/ConvertingPharmacoSetToGDR.html","id":"sessioninfo","dir":"Articles","previous_headings":"","what":"SessionInfo","title":"Converting PharmacoSet Drug Response Data into gDR object","text":"","code":"sessionInfo() #> R version 4.3.0 (2023-04-21) #> Platform: x86_64-pc-linux-gnu (64-bit) #> Running under: Ubuntu 22.04.3 LTS #>  #> Matrix products: default #> BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3  #> LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;  LAPACK version 3.10.0 #>  #> locale: #>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               #>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     #>  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8    #>  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  #>  [9] LC_ADDRESS=C               LC_TELEPHONE=C             #> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C        #>  #> time zone: Etc/UTC #> tzcode source: system (glibc) #>  #> attached base packages: #> [1] stats4    stats     graphics  grDevices utils     datasets  methods   #> [8] base      #>  #> other attached packages: #>  [1] gDRimport_1.5.2             PharmacoGx_3.6.0            #>  [3] CoreGx_2.6.1                SummarizedExperiment_1.32.0 #>  [5] Biobase_2.62.0              GenomicRanges_1.54.1        #>  [7] GenomeInfoDb_1.38.8         IRanges_2.36.0              #>  [9] S4Vectors_0.40.2            MatrixGenerics_1.14.0       #> [11] matrixStats_1.4.1           BiocGenerics_0.48.1         #>  #> loaded via a namespace (and not attached): #>   [1] RColorBrewer_1.1-3          jsonlite_1.8.9              #>   [3] MultiAssayExperiment_1.28.0 magrittr_2.0.3              #>   [5] rmarkdown_2.29              fs_1.6.5                    #>   [7] zlibbioc_1.48.2             ragg_1.2.7                  #>   [9] vctrs_0.6.5                 memoise_2.0.1               #>  [11] magicaxis_2.4.5             RCurl_1.98-1.16             #>  [13] htmltools_0.5.8.1           S4Arrays_1.2.1              #>  [15] plotrix_3.8-4               SparseArray_1.2.4           #>  [17] sass_0.4.9                  pracma_2.4.4                #>  [19] KernSmooth_2.23-20          bslib_0.8.0                 #>  [21] htmlwidgets_1.6.4           desc_1.4.3                  #>  [23] plyr_1.8.9                  testthat_3.2.1              #>  [25] cachem_1.1.0                igraph_2.1.1                #>  [27] mime_0.12                   lifecycle_1.0.4             #>  [29] piano_2.18.0                pkgconfig_2.0.3             #>  [31] Matrix_1.6-5                R6_2.5.1                    #>  [33] fastmap_1.2.0               GenomeInfoDbData_1.2.11     #>  [35] shiny_1.9.1                 digest_0.6.37               #>  [37] colorspace_2.1-1            rprojroot_2.0.4             #>  [39] pkgload_1.3.4               textshaping_0.3.7           #>  [41] SnowballC_0.7.1             fansi_1.0.6                 #>  [43] abind_1.4-8                 coop_0.6-3                  #>  [45] compiler_4.3.0              downloader_0.4              #>  [47] marray_1.80.0               backports_1.5.0             #>  [49] BiocParallel_1.36.0         gDRutils_1.5.2              #>  [51] bench_1.1.3                 qs_0.27.2                   #>  [53] gplots_3.2.0                maps_3.4.2                  #>  [55] MASS_7.3-58.4               DelayedArray_0.28.0         #>  [57] gtools_3.9.5                caTools_1.18.3              #>  [59] tools_4.3.0                 NISTunits_1.0.1             #>  [61] httpuv_1.6.15               relations_0.6-13            #>  [63] glue_1.8.0                  promises_1.3.0              #>  [65] grid_4.3.0                  checkmate_2.3.2             #>  [67] cluster_2.1.4               reshape2_1.4.4              #>  [69] fgsea_1.28.0                generics_0.1.3              #>  [71] gtable_0.3.6                sm_2.2-6.0                  #>  [73] data.table_1.16.2           RApiSerialize_0.1.4         #>  [75] stringfish_0.16.0           utf8_1.2.4                  #>  [77] XVector_0.42.0              RANN_2.6.2                  #>  [79] pillar_1.9.0                stringr_1.5.1               #>  [81] limma_3.58.1                BumpyMatrix_1.10.0          #>  [83] later_1.3.2                 dplyr_1.1.4                 #>  [85] lattice_0.21-8              tidyselect_1.2.1            #>  [87] knitr_1.48                  xfun_0.49                   #>  [89] shinydashboard_0.7.2        statmod_1.5.0               #>  [91] brio_1.1.4                  DT_0.33                     #>  [93] visNetwork_2.1.2            stringi_1.8.4               #>  [95] yaml_2.3.10                 boot_1.3-28.1               #>  [97] evaluate_1.0.1              codetools_0.2-19            #>  [99] lsa_0.73.3                  tibble_3.2.1                #> [101] cli_3.6.3                   RcppParallel_5.1.7          #> [103] xtable_1.8-4                systemfonts_1.0.5           #> [105] munsell_0.5.1               jquerylib_0.1.4             #> [107] Rcpp_1.0.13-1               mapproj_1.2.11              #> [109] parallel_4.3.0              sets_1.0-25                 #> [111] pkgdown_2.0.7               ggplot2_3.5.1               #> [113] assertthat_0.2.1            bitops_1.0-9                #> [115] slam_0.1-54                 celestial_1.4.6             #> [117] scales_1.3.0                purrr_1.0.2                 #> [119] crayon_1.5.3                rlang_1.1.4                 #> [121] cowplot_1.1.3               fastmatch_1.1-4             #> [123] shinyjs_2.1.0"},{"path":"https://gdrplatform.github.io/gDRimport/articles/gDRimport.html","id":"overview","dir":"Articles","previous_headings":"","what":"Overview","title":"gDRimport","text":"gDRimport package part gDR suite. helps prepare raw drug response data downstream processing. mainly contains helper functions importing/loading/validating dose response data provided different file formats.","code":""},{"path":[]},{"path":"https://gdrplatform.github.io/gDRimport/articles/gDRimport.html","id":"test-data","dir":"Articles","previous_headings":"Use Cases","what":"Test Data","title":"gDRimport","text":"currently four test datasets can used see ’s expected input data gDRimport.","code":"# primary test data td1 <- get_test_data() summary(td1) ##        Length         Class          Mode  ##             1 gdr_test_data            S4 td1 ## class: gdr_test_data  ## slots: manifest_path result_path template_path ref_m_df ref_r1_r2 ref_r1 ref_t1_t2 ref_t1 # test data in Tecan format td2 <- get_test_Tecan_data() summary(td2) ##          Length Class  Mode      ## m_file   1      -none- character ## r_files  1      -none- character ## t_files  1      -none- character ## ref_m_df 1      -none- character ## ref_r_df 1      -none- character ## ref_t_df 1      -none- character # test data in D300 format td3 <- get_test_D300_data() summary(td3) ##        Length Class  Mode ## f_96w  6      -none- list ## f_384w 6      -none- list # test data obtained from EnVision td4 <- get_test_EnVision_data() summary(td4) ##            Length Class  Mode      ## m_file      1     -none- character ## r_files    28     -none- character ## t_files     2     -none- character ## ref_l_path  1     -none- character"},{"path":"https://gdrplatform.github.io/gDRimport/articles/gDRimport.html","id":"load-data","dir":"Articles","previous_headings":"Use Cases","what":"Load data","title":"gDRimport","text":"load_data key function. wraps load_manifest, load_templates load_results functions supports different file formats.","code":"ml <- load_manifest(manifest_path(td1)) summary(ml) ##         Length Class      Mode ## data     4     data.table list ## headers 27     -none-     list t_df <- load_templates(template_path(td1)) summary(t_df) ##    WellRow           WellColumn          Gnumber          Concentration      ##  Length:768         Length:768         Length:768         Length:768         ##  Class :character   Class :character   Class :character   Class :character   ##  Mode  :character   Mode  :character   Mode  :character   Mode  :character   ##   Gnumber_2         Concentration_2      Template         ##  Length:768         Length:768         Length:768         ##  Class :character   Class :character   Class :character   ##  Mode  :character   Mode  :character   Mode  :character r_df <- suppressMessages(load_results(result_path(td1))) summary(r_df) ##    Barcode            WellRow            WellColumn     ReadoutValue     ##  Length:4587        Length:4587        Min.   : 1.00   Min.   :  12627   ##  Class :character   Class :character   1st Qu.: 6.50   1st Qu.:  67905   ##  Mode  :character   Mode  :character   Median :12.00   Median : 140865   ##                                        Mean   :12.49   Mean   : 263996   ##                                        3rd Qu.:18.00   3rd Qu.: 324707   ##                                        Max.   :24.00   Max.   :2423054   ##  BackgroundValue ##  Min.   :332.0   ##  1st Qu.:351.0   ##  Median :374.0   ##  Mean   :453.2   ##  3rd Qu.:570.0   ##  Max.   :704.0 l_tbl <-   suppressMessages(     load_data(manifest_path(td1), template_path(td1), result_path(td1))) summary(l_tbl) ##            Length Class      Mode ## manifest   4      data.table list ## treatments 7      data.table list ## data       5      data.table list"},{"path":"https://gdrplatform.github.io/gDRimport/articles/gDRimport.html","id":"prism","dir":"Articles","previous_headings":"","what":"PRISM","title":"gDRimport","text":"PRISM, Multiplexed cancer cell line screening platform, facilitates rapid screening broad spectrum drugs across 900 human cancer cell line models, employing high-throughput, multiplexed approach. Publicly available PRISM data can downloaded DepMap website (DepMap). gDRimport package provides support processing PRISM data two levels: LEVEL5 LEVEL6. LEVEL5 Data: format encapsulates information drugs, cell lines, viability within single file. process LEVEL5 PRISM data, can use convert_LEVEL5_prism_to_gDR_input() function. function transforms cleans data also executes gDR pipeline analysis. LEVEL6 Data: LEVEL6, PRISM data distributed across three separate files: prism_data: containing collapsed log fold change data viability assays. cell_line_data: providing information cell lines. treatment_data: containing treatment data. Processing LEVEL6 PRISM data can accomplished using convert_LEVEL6_prism_to_gDR_input() function, requires paths three files input arguments.","code":""},{"path":"https://gdrplatform.github.io/gDRimport/articles/gDRimport.html","id":"processing-level5-prism-data","dir":"Articles","previous_headings":"PRISM","what":"Processing LEVEL5 PRISM Data","title":"gDRimport","text":"process LEVEL5 PRISM data, can use following function: Replace “path_to_file” actual path LEVEL5 PRISM data file. function handle transformation, cleaning, execution gDR pipeline automatically.","code":"convert_LEVEL5_prism_to_gDR_input(\"path_to_file\")"},{"path":"https://gdrplatform.github.io/gDRimport/articles/gDRimport.html","id":"processing-level6-prism-data","dir":"Articles","previous_headings":"PRISM","what":"Processing LEVEL6 PRISM Data","title":"gDRimport","text":"process LEVEL6 PRISM data, can use following function: Replace “prism_data_path”, “cell_line_data_path”, “treatment_data_path” respective paths LEVEL6 PRISM data files.","code":"convert_LEVEL6_prism_to_gDR_input(\"prism_data_path\", \"cell_line_data_path\", \"treatment_data_path\")"},{"path":"https://gdrplatform.github.io/gDRimport/articles/gDRimport.html","id":"package-installation","dir":"Articles","previous_headings":"PRISM","what":"Package installation","title":"gDRimport","text":"function installAllDeps assists installing package dependencies.","code":""},{"path":"https://gdrplatform.github.io/gDRimport/articles/gDRimport.html","id":"sessioninfo","dir":"Articles","previous_headings":"","what":"SessionInfo","title":"gDRimport","text":"","code":"sessionInfo() ## R version 4.3.0 (2023-04-21) ## Platform: x86_64-pc-linux-gnu (64-bit) ## Running under: Ubuntu 22.04.3 LTS ##  ## Matrix products: default ## BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3  ## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;  LAPACK version 3.10.0 ##  ## locale: ##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               ##  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     ##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8    ##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  ##  [9] LC_ADDRESS=C               LC_TELEPHONE=C             ## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C        ##  ## time zone: Etc/UTC ## tzcode source: system (glibc) ##  ## attached base packages: ## [1] stats     graphics  grDevices utils     datasets  methods   base      ##  ## other attached packages: ## [1] gDRimport_1.5.2  BiocStyle_2.30.0 ##  ## loaded via a namespace (and not attached): ##  [1] SummarizedExperiment_1.32.0 xfun_0.49                   ##  [3] bslib_0.8.0                 Biobase_2.62.0              ##  [5] lattice_0.21-8              vctrs_0.6.5                 ##  [7] tools_4.3.0                 bitops_1.0-9                ##  [9] stats4_4.3.0                tibble_3.2.1                ## [11] fansi_1.0.6                 pkgconfig_2.0.3             ## [13] Matrix_1.6-5                data.table_1.16.2           ## [15] checkmate_2.3.2             desc_1.4.3                  ## [17] S4Vectors_0.40.2            gDRutils_1.5.2              ## [19] rematch_2.0.0               readxl_1.4.3                ## [21] assertthat_0.2.1            lifecycle_1.0.4             ## [23] GenomeInfoDbData_1.2.11     compiler_4.3.0              ## [25] textshaping_0.3.7           GenomeInfoDb_1.38.8         ## [27] htmltools_0.5.8.1           sass_0.4.9                  ## [29] RCurl_1.98-1.16             yaml_2.3.10                 ## [31] pillar_1.9.0                pkgdown_2.0.7               ## [33] crayon_1.5.3                jquerylib_0.1.4             ## [35] DelayedArray_0.28.0         cachem_1.1.0                ## [37] abind_1.4-8                 digest_0.6.37               ## [39] purrr_1.0.2                 bookdown_0.37               ## [41] fastmap_1.2.0               grid_4.3.0                  ## [43] cli_3.6.3                   SparseArray_1.2.4           ## [45] magrittr_2.0.3              S4Arrays_1.2.1              ## [47] utf8_1.2.4                  backports_1.5.0             ## [49] rmarkdown_2.29              lambda.r_1.2.4              ## [51] XVector_0.42.0              matrixStats_1.4.1           ## [53] futile.logger_1.4.3         cellranger_1.1.0            ## [55] ragg_1.2.7                  memoise_2.0.1               ## [57] evaluate_1.0.1              knitr_1.48                  ## [59] GenomicRanges_1.54.1        IRanges_2.36.0              ## [61] rlang_1.1.4                 futile.options_1.0.1        ## [63] glue_1.8.0                  BiocManager_1.30.22         ## [65] formatR_1.14                BiocGenerics_0.48.1         ## [67] jsonlite_1.8.9              R6_2.5.1                    ## [69] MatrixGenerics_1.14.0       systemfonts_1.0.5           ## [71] fs_1.6.5                    zlibbioc_1.48.2"},{"path":"https://gdrplatform.github.io/gDRimport/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Arkadiusz Gladki. Author, maintainer. Bartosz Czech. Author. Marc Hafner. Author. Sergiu Mocanu. Author. Dariusz Scigocki. Author. Allison Vuong. Author. Luca Gerosa. Author. Janina Smola. Author.","code":""},{"path":"https://gdrplatform.github.io/gDRimport/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Gladki , Czech B, Hafner M, Mocanu S, Scigocki D, Vuong , Gerosa L, Smola J (2024). gDRimport: Package handling import dose-response data. https://github.com/gdrplatform/gDRimport, https://gdrplatform.github.io/gDRimport/.","code":"@Manual{,   title = {gDRimport: Package for handling the import of dose-response data},   author = {Arkadiusz Gladki and Bartosz Czech and Marc Hafner and Sergiu Mocanu and Dariusz Scigocki and Allison Vuong and Luca Gerosa and Janina Smola},   year = {2024},   note = {https://github.com/gdrplatform/gDRimport, https://gdrplatform.github.io/gDRimport/}, }"},{"path":"https://gdrplatform.github.io/gDRimport/index.html","id":"gdrimport","dir":"","previous_headings":"","what":"Package for handling the import of dose-response data","title":"Package for handling the import of dose-response data","text":"Package handling import dose-response data","code":""},{"path":"https://gdrplatform.github.io/gDRimport/index.html","id":"website","dir":"","previous_headings":"","what":"Website","title":"Package for handling the import of dose-response data","text":"package website available link.","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/are_template_sheets_valid.html","id":null,"dir":"Reference","previous_headings":"","what":"are template sheet valid? — are_template_sheets_valid","title":"are template sheet valid? — are_template_sheets_valid","text":"template sheet valid?","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/are_template_sheets_valid.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"are template sheet valid? — are_template_sheets_valid","text":"","code":"are_template_sheets_valid(ts)"},{"path":"https://gdrplatform.github.io/gDRimport/reference/are_template_sheets_valid.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"are template sheet valid? — are_template_sheets_valid","text":"ts list (per file) template sheets","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/are_template_sheets_valid.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"are template sheet valid? — are_template_sheets_valid","text":"logical flag","code":""},{"path":[]},{"path":"https://gdrplatform.github.io/gDRimport/reference/check_metadata_against_spaces.html","id":null,"dir":"Reference","previous_headings":"","what":"Check metadata against spaces — check_metadata_against_spaces","title":"Check metadata against spaces — check_metadata_against_spaces","text":"Check metadata spaces","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/check_metadata_against_spaces.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check metadata against spaces — check_metadata_against_spaces","text":"","code":"check_metadata_against_spaces(corrected_names, df_name)"},{"path":"https://gdrplatform.github.io/gDRimport/reference/check_metadata_against_spaces.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check metadata against spaces — check_metadata_against_spaces","text":"corrected_names charvec corrected colnames df df_name name data.table (\"\" default)","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/check_metadata_against_spaces.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check metadata against spaces — check_metadata_against_spaces","text":"charvec corrected colnames df","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/check_metadata_field_names.html","id":null,"dir":"Reference","previous_headings":"","what":"Check metadata field names — check_metadata_field_names","title":"Check metadata field names — check_metadata_field_names","text":"Check metadata field names","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/check_metadata_field_names.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check metadata field names — check_metadata_field_names","text":"","code":"check_metadata_field_names(corrected_names, df_name)"},{"path":"https://gdrplatform.github.io/gDRimport/reference/check_metadata_field_names.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check metadata field names — check_metadata_field_names","text":"corrected_names charvec corrected colnames df df_name name data.table (\"\" default)","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/check_metadata_field_names.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check metadata field names — check_metadata_field_names","text":"charvec corrected colnames df","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/check_metadata_headers.html","id":null,"dir":"Reference","previous_headings":"","what":"Check whether metadata headers are correct and make fixes if needed — check_metadata_headers","title":"Check whether metadata headers are correct and make fixes if needed — check_metadata_headers","text":"Check whether metadata headers correct make fixes needed","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/check_metadata_headers.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check whether metadata headers are correct and make fixes if needed — check_metadata_headers","text":"","code":"check_metadata_headers(corrected_names, df_name)"},{"path":"https://gdrplatform.github.io/gDRimport/reference/check_metadata_headers.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check whether metadata headers are correct and make fixes if needed — check_metadata_headers","text":"corrected_names charvec corrected colnames df df_name name data.table (\"\" default)","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/check_metadata_headers.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check whether metadata headers are correct and make fixes if needed — check_metadata_headers","text":"charvec corrected colnames df","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/check_metadata_names.html","id":null,"dir":"Reference","previous_headings":"","what":"check_metadata_names — check_metadata_names","title":"check_metadata_names — check_metadata_names","text":"Check whether metadata names correct","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/check_metadata_names.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"check_metadata_names — check_metadata_names","text":"","code":"check_metadata_names(col_df, df_name = \"\", df_type = NULL)"},{"path":"https://gdrplatform.github.io/gDRimport/reference/check_metadata_names.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"check_metadata_names — check_metadata_names","text":"col_df character colnames df df_name name data.table (\"\" default) df_type type data.table (NULL default)","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/check_metadata_names.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"check_metadata_names — check_metadata_names","text":"charvec corrected colnames df","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/check_metadata_names.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"check_metadata_names — check_metadata_names","text":"","code":"td <- get_test_data()  m_file <- manifest_path(td)  m_data <- read_excel_to_dt(m_file)  result <- check_metadata_names(col_df = colnames(m_data))"},{"path":"https://gdrplatform.github.io/gDRimport/reference/check_metadata_req_col_names.html","id":null,"dir":"Reference","previous_headings":"","what":"Check metadata for required column names — check_metadata_req_col_names","title":"Check metadata for required column names — check_metadata_req_col_names","text":"Check metadata required column names","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/check_metadata_req_col_names.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check metadata for required column names — check_metadata_req_col_names","text":"","code":"check_metadata_req_col_names(col_df, df_name, df_type)"},{"path":"https://gdrplatform.github.io/gDRimport/reference/check_metadata_req_col_names.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check metadata for required column names — check_metadata_req_col_names","text":"col_df charvec corrected colnames df df_name name data.table (\"\" default) df_type type data.table (NULL default)","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/check_metadata_req_col_names.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check metadata for required column names — check_metadata_req_col_names","text":"NULL invisibly.","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/convert_LEVEL5_prism_to_gDR_input.html","id":null,"dir":"Reference","previous_headings":"","what":"Load, convert and process the level 5 PRISM data into a gDR input — convert_LEVEL5_prism_to_gDR_input","title":"Load, convert and process the level 5 PRISM data into a gDR input — convert_LEVEL5_prism_to_gDR_input","text":"Load, convert process level 5 PRISM data gDR input","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/convert_LEVEL5_prism_to_gDR_input.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Load, convert and process the level 5 PRISM data into a gDR input — convert_LEVEL5_prism_to_gDR_input","text":"","code":"convert_LEVEL5_prism_to_gDR_input(prism_data_path, readout_min = 1.03)"},{"path":"https://gdrplatform.github.io/gDRimport/reference/convert_LEVEL5_prism_to_gDR_input.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Load, convert and process the level 5 PRISM data into a gDR input — convert_LEVEL5_prism_to_gDR_input","text":"prism_data_path path PRISM LEVEL5 csv file data readout_min minimum ReadoutValue","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/convert_LEVEL5_prism_to_gDR_input.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Load, convert and process the level 5 PRISM data into a gDR input — convert_LEVEL5_prism_to_gDR_input","text":"data.table object input data gDR pipeline","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/convert_LEVEL5_prism_to_gDR_input.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Load, convert and process the level 5 PRISM data into a gDR input — convert_LEVEL5_prism_to_gDR_input","text":"","code":"prism_data <- system.file(\"testdata/prism_sa.csv\", package = \"gDRimport\")  convert_LEVEL5_prism_to_gDR_input(prism_data) #>         clid Duration ReadoutValue BackgroundValue      Gnumber Concentration #>       <char>    <num>        <num>           <num>       <char>         <num> #> 1: some_clid      120         1.03               0 some_gnumber      0.003201 #> 2: some_clid      120         1.00               0      vehicle      0.000000 #>    masked #>    <lgcl> #> 1:  FALSE #> 2:  FALSE"},{"path":"https://gdrplatform.github.io/gDRimport/reference/convert_LEVEL6_prism_to_gDR_input.html","id":null,"dir":"Reference","previous_headings":"","what":"Load, convert and process the level 6 PRISM data into a gDR input — convert_LEVEL6_prism_to_gDR_input","title":"Load, convert and process the level 6 PRISM data into a gDR input — convert_LEVEL6_prism_to_gDR_input","text":"Load, convert process level 6 PRISM data gDR input","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/convert_LEVEL6_prism_to_gDR_input.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Load, convert and process the level 6 PRISM data into a gDR input — convert_LEVEL6_prism_to_gDR_input","text":"","code":"convert_LEVEL6_prism_to_gDR_input(   prism_data_path,   cell_line_data_path,   treatment_data_path,   readout_min = 1.03 )"},{"path":"https://gdrplatform.github.io/gDRimport/reference/convert_LEVEL6_prism_to_gDR_input.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Load, convert and process the level 6 PRISM data into a gDR input — convert_LEVEL6_prism_to_gDR_input","text":"prism_data_path path PRISM LEVEL6 csv file collapsed log fold change data cell_line_data_path path cell line info data treatment_data_path path collapsed treatment info data readout_min minimum ReadoutValue","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/convert_LEVEL6_prism_to_gDR_input.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Load, convert and process the level 6 PRISM data into a gDR input — convert_LEVEL6_prism_to_gDR_input","text":"data.table object input data gDR pipeline","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/convert_LEVEL6_prism_to_gDR_input.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Load, convert and process the level 6 PRISM data into a gDR input — convert_LEVEL6_prism_to_gDR_input","text":"","code":"prism_data_path <- system.file(\"testdata/prism_collapsed_LOGFC.csv\", package = \"gDRimport\")  cell_line_data_path <- system.file(\"testdata/prism_cell_lines.csv\", package = \"gDRimport\")  treatment_data_path <- system.file(\"testdata/prism_treatment.csv\", package = \"gDRimport\")  convert_LEVEL6_prism_to_gDR_input(prism_data_path, cell_line_data_path, treatment_data_path) #>         clid        Gnumber       DrugName      drug_moa Duration Concentration #>       <char>         <char>         <char>        <char>    <num>         <num> #> 1: some_clid some_drug_name some_drug_name some_drug_moa      120      2.325889 #> 2: some_clid        vehicle        vehicle       vehicle      120      0.000000 #>    ReadoutValue masked #>           <num> <lgcl> #> 1:    0.9892612  FALSE #> 2:    1.0000000  FALSE"},{"path":"https://gdrplatform.github.io/gDRimport/reference/convert_MAE_to_PSet.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert MultiAssayExperiment to TreatmentResponseExperiment — convert_MAE_to_PSet","title":"Convert MultiAssayExperiment to TreatmentResponseExperiment — convert_MAE_to_PSet","text":"function converts MultiAssayExperiment generated gDR TreatmentResponseExperiment use PharmacoGx package. resulting PharmacoSet can used pharmacogenomic analysis drug response.","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/convert_MAE_to_PSet.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert MultiAssayExperiment to TreatmentResponseExperiment — convert_MAE_to_PSet","text":"","code":"convert_MAE_to_PSet(mae, pset_name)"},{"path":"https://gdrplatform.github.io/gDRimport/reference/convert_MAE_to_PSet.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert MultiAssayExperiment to TreatmentResponseExperiment — convert_MAE_to_PSet","text":"mae MultiAssayExperiment object generated gDR. pset_name character string specifying name resulting PharmacoSet object.","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/convert_MAE_to_PSet.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert MultiAssayExperiment to TreatmentResponseExperiment — convert_MAE_to_PSet","text":"PharmacoSet object.","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/convert_MAE_to_PSet.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Convert MultiAssayExperiment to TreatmentResponseExperiment — convert_MAE_to_PSet","text":"","code":"# Convert a MultiAssayExperiment object to a PharmacoSet object m <- 20 n <- 10 rnames <- LETTERS[1:m] cnames <- letters[1:n] ref_gr_value <-  matrix(runif(m * n), nrow = m, ncol = n, dimnames = list(rnames, cnames)) se <- SummarizedExperiment::SummarizedExperiment(assays = list(RefGRvalue = ref_gr_value),                                                  rowData = S4Vectors::DataFrame(rnames),                                                  colData = S4Vectors::DataFrame(cnames)) mae <- MultiAssayExperiment::MultiAssayExperiment(experiments = list(\"single-agent\" = se)) convert_MAE_to_PSet(mae, \"my_pset\") #> <PharmacoSet> #> Name:  my_pset  #> Date Created:  Thu Nov  7 10:36:41 2024  #> Number of samples:  10  #> Molecular profiles: #>    A MultiAssayExperiment object of 1 listed #>    experiment with a user-defined name and respective class. #>    Containing an ExperimentList class object of length 1: #>    [1] emptySE: SummarizedExperiment with 0 rows and 10 columns  #> Treatment response: #>    <TreatmentResponseExperiment>  #>   dim:  20 10  #>   assays(1): RefGRvalue  #>   rownames(20): A B ... S T  #>   rowData(2): treatmentid rnames  #>   colnames(10): a b c ... h i j  #>   colData(2): sampleid cnames  #>   metadata(0): none"},{"path":"https://gdrplatform.github.io/gDRimport/reference/convert_pset_to_df.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert a PharmacoSet to a data.table that is prepare for input into gDR pipeline — convert_pset_to_df","title":"Convert a PharmacoSet to a data.table that is prepare for input into gDR pipeline — convert_pset_to_df","text":"Convert PharmacoSet data.table prepare input gDR pipeline","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/convert_pset_to_df.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert a PharmacoSet to a data.table that is prepare for input into gDR pipeline — convert_pset_to_df","text":"","code":"convert_pset_to_df(pharmacoset, run_parallel = TRUE, workers = 2L)"},{"path":"https://gdrplatform.github.io/gDRimport/reference/convert_pset_to_df.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert a PharmacoSet to a data.table that is prepare for input into gDR pipeline — convert_pset_to_df","text":"pharmacoset PharmacoSet object run_parallel logical, TRUE (default) run functions Parallel, FALSE run serial workers integer, number workers defaults 2L run_parallel TRUE","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/convert_pset_to_df.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert a PharmacoSet to a data.table that is prepare for input into gDR pipeline — convert_pset_to_df","text":"data.table PharmacoSet's dose response data column names aligned gDR standard","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/convert_pset_to_df.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Convert a PharmacoSet to a data.table that is prepare for input into gDR pipeline — convert_pset_to_df","text":"Jermiah Joseph -- collaboration BHKLab","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/convert_pset_to_df.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Convert a PharmacoSet to a data.table that is prepare for input into gDR pipeline — convert_pset_to_df","text":"","code":"pset <- suppressMessages(getPSet(   \"Tavor_2020\",    psetDir = system.file(\"extdata/pset\", package = \"gDRimport\"),   use_local_PSets_list = TRUE )) dt <- convert_pset_to_df(pset) gDRutils::reset_env_identifiers()"},{"path":"https://gdrplatform.github.io/gDRimport/reference/correct_template_sheets.html","id":null,"dir":"Reference","previous_headings":"","what":"Correct names of the template sheets (if required) — correct_template_sheets","title":"Correct names of the template sheets (if required) — correct_template_sheets","text":"Correct names template sheets (required)","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/correct_template_sheets.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Correct names of the template sheets (if required) — correct_template_sheets","text":"","code":"correct_template_sheets(tfiles)"},{"path":"https://gdrplatform.github.io/gDRimport/reference/correct_template_sheets.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Correct names of the template sheets (if required) — correct_template_sheets","text":"tfiles charvec paths template files","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/correct_template_sheets.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Correct names of the template sheets (if required) — correct_template_sheets","text":"charvec paths corrected sheet names","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/detect_file_format.html","id":null,"dir":"Reference","previous_headings":"","what":"Detect format of results data — detect_file_format","title":"Detect format of results data — detect_file_format","text":"Detect format results data","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/detect_file_format.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Detect format of results data — detect_file_format","text":"","code":"detect_file_format(results_file)"},{"path":"https://gdrplatform.github.io/gDRimport/reference/detect_file_format.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Detect format of results data — detect_file_format","text":"results_file path results data","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/detect_file_format.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Detect format of results data — detect_file_format","text":"string detected file format","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/detect_file_format.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Detect format of results data — detect_file_format","text":"","code":"td2 <- get_test_Tecan_data() detect_file_format(td2$r_files[1]) #> New names: #> • `` -> `...2` #> • `` -> `...3` #> • `` -> `...4` #> • `` -> `...6` #> • `` -> `...7` #> • `` -> `...8` #> • `` -> `...9` #> • `` -> `...10` #> • `` -> `...11` #> [1] \"Tecan\""},{"path":"https://gdrplatform.github.io/gDRimport/reference/dot-check_against_single_template_sheet.html","id":null,"dir":"Reference","previous_headings":"","what":"Evaluate if template file with single sheet is present,\nif the name of the sheet is correct and if it can be fixed — .check_against_single_template_sheet","title":"Evaluate if template file with single sheet is present,\nif the name of the sheet is correct and if it can be fixed — .check_against_single_template_sheet","text":"get sheets given set XLS files","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/dot-check_against_single_template_sheet.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Evaluate if template file with single sheet is present,\nif the name of the sheet is correct and if it can be fixed — .check_against_single_template_sheet","text":"","code":".check_against_single_template_sheet(ts)"},{"path":"https://gdrplatform.github.io/gDRimport/reference/dot-check_against_single_template_sheet.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Evaluate if template file with single sheet is present,\nif the name of the sheet is correct and if it can be fixed — .check_against_single_template_sheet","text":"ts list template sheets info","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/dot-check_against_single_template_sheet.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Evaluate if template file with single sheet is present,\nif the name of the sheet is correct and if it can be fixed — .check_against_single_template_sheet","text":"logical flag","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/dot-check_file_structure.html","id":null,"dir":"Reference","previous_headings":"","what":"Check the structure of raw data — .check_file_structure","title":"Check the structure of raw data — .check_file_structure","text":"Check structure raw data","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/dot-check_file_structure.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check the structure of raw data — .check_file_structure","text":"","code":".check_file_structure(   df,   filename,   sheet_name,   readout_offset,   n_row,   n_col,   bcode_idx,   bcode_col )"},{"path":"https://gdrplatform.github.io/gDRimport/reference/dot-check_file_structure.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check the structure of raw data — .check_file_structure","text":"NULL invisibly.","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/dot-createPseudoData.html","id":null,"dir":"Reference","previous_headings":"","what":"Add in pseudo-data for duration and cell reference division time — .createPseudoData","title":"Add in pseudo-data for duration and cell reference division time — .createPseudoData","text":"Add pseudo-data duration cell reference division time","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/dot-createPseudoData.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add in pseudo-data for duration and cell reference division time — .createPseudoData","text":"","code":".createPseudoData(dt)"},{"path":"https://gdrplatform.github.io/gDRimport/reference/dot-createPseudoData.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add in pseudo-data for duration and cell reference division time — .createPseudoData","text":"data.table","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/dot-extractDoseResponse.html","id":null,"dir":"Reference","previous_headings":"","what":"Get dose and viability readouts and melt into large data table — .extractDoseResponse","title":"Get dose and viability readouts and melt into large data table — .extractDoseResponse","text":"Get dose viability readouts melt large data table","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/dot-extractDoseResponse.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get dose and viability readouts and melt into large data table — .extractDoseResponse","text":"","code":".extractDoseResponse(pset)"},{"path":"https://gdrplatform.github.io/gDRimport/reference/dot-extractDoseResponse.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get dose and viability readouts and melt into large data table — .extractDoseResponse","text":"data.table dose-response data","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/dot-extract_or_create_assay.html","id":null,"dir":"Reference","previous_headings":"","what":"Extracts an assay from a SummarizedExperiment object or creates a new one if it does not exist — .extract_or_create_assay","title":"Extracts an assay from a SummarizedExperiment object or creates a new one if it does not exist — .extract_or_create_assay","text":"function takes SummarizedExperiment object assay name input. specified assay already exists SummarizedExperiment object, returned. Otherwise, new assay specified name created added SummarizedExperiment object. new assay initialized NA values. useful multiple Summarized Experiments given MAE assays. necessary assays Summarized Experiments order convert MAE PSet.","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/dot-extract_or_create_assay.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Extracts an assay from a SummarizedExperiment object or creates a new one if it does not exist — .extract_or_create_assay","text":"","code":".extract_or_create_assay(SE, assay_name)"},{"path":"https://gdrplatform.github.io/gDRimport/reference/dot-extract_or_create_assay.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Extracts an assay from a SummarizedExperiment object or creates a new one if it does not exist — .extract_or_create_assay","text":"SE SummarizedExperiment object assay_name character string specifying name assay extract create","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/dot-extract_or_create_assay.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Extracts an assay from a SummarizedExperiment object or creates a new one if it does not exist — .extract_or_create_assay","text":"SummarizedExperiment object specified assay","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/dot-fill_empty_wells.html","id":null,"dir":"Reference","previous_headings":"","what":"Correct plates with not fully filled readout values — .fill_empty_wells","title":"Correct plates with not fully filled readout values — .fill_empty_wells","text":"Correct plates fully filled readout values","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/dot-fill_empty_wells.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Correct plates with not fully filled readout values — .fill_empty_wells","text":"","code":".fill_empty_wells(   df,   plate_rows,   data_rows,   exp_row,   exp_col,   numeric_regex = \"^\\\\d+$\" )"},{"path":"https://gdrplatform.github.io/gDRimport/reference/dot-fill_empty_wells.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Correct plates with not fully filled readout values — .fill_empty_wells","text":"data.table corrected plates data","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/dot-get_plate_size.html","id":null,"dir":"Reference","previous_headings":"","what":"Get plate size — .get_plate_size","title":"Get plate size — .get_plate_size","text":"Get plate size","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/dot-get_plate_size.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get plate size — .get_plate_size","text":"","code":".get_plate_size(df)"},{"path":"https://gdrplatform.github.io/gDRimport/reference/dot-get_plate_size.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get plate size — .get_plate_size","text":"charvec plate dims","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/dot-get_plate_size.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Get plate size — .get_plate_size","text":"plate sizes assume 1.5x nrows = ncolumns.","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/dot-removeNegatives.html","id":null,"dir":"Reference","previous_headings":"","what":"Remove negative viabilities — .removeNegatives","title":"Remove negative viabilities — .removeNegatives","text":"Remove negative viabilities","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/dot-removeNegatives.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Remove negative viabilities — .removeNegatives","text":"","code":".removeNegatives(dataset)"},{"path":"https://gdrplatform.github.io/gDRimport/reference/dot-removeNegatives.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Remove negative viabilities — .removeNegatives","text":"data.table positive values column ReadoutValue","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/dot-standardize_untreated_values.html","id":null,"dir":"Reference","previous_headings":"","what":"Standardize untreated values to ignore cases — .standardize_untreated_values","title":"Standardize untreated values to ignore cases — .standardize_untreated_values","text":"Standardize untreated values ignore cases","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/dot-standardize_untreated_values.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Standardize untreated values to ignore cases — .standardize_untreated_values","text":"","code":".standardize_untreated_values(df)"},{"path":"https://gdrplatform.github.io/gDRimport/reference/dot-standardize_untreated_values.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Standardize untreated values to ignore cases — .standardize_untreated_values","text":"data.table standardized untreated values","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/enhance_raw_edited_EnVision_df.html","id":null,"dir":"Reference","previous_headings":"","what":"Enhance raw edited EnVision data.table — enhance_raw_edited_EnVision_df","title":"Enhance raw edited EnVision data.table — enhance_raw_edited_EnVision_df","text":"Enhance raw edited EnVision data.table","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/enhance_raw_edited_EnVision_df.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Enhance raw edited EnVision data.table — enhance_raw_edited_EnVision_df","text":"","code":"enhance_raw_edited_EnVision_df(df, barcode_col, headers)"},{"path":"https://gdrplatform.github.io/gDRimport/reference/enhance_raw_edited_EnVision_df.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Enhance raw edited EnVision data.table — enhance_raw_edited_EnVision_df","text":"df raw data.table barcode_col column number barcode data headers list headersa","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/enhance_raw_edited_EnVision_df.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Enhance raw edited EnVision data.table — enhance_raw_edited_EnVision_df","text":"data.table derived EnVision data","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/fix_typos_with_reference.html","id":null,"dir":"Reference","previous_headings":"","what":"Fix typos using reference data — fix_typos_with_reference","title":"Fix typos using reference data — fix_typos_with_reference","text":"Fix typos using reference data Evaluate given list ids try update ","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/fix_typos_with_reference.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fix typos using reference data — fix_typos_with_reference","text":"","code":"fix_typos_with_reference(   data,   ref,   method = c(\"exact\", \"grepl\", \"adist\"),   fix_underscores = FALSE )"},{"path":"https://gdrplatform.github.io/gDRimport/reference/fix_typos_with_reference.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Fix typos using reference data — fix_typos_with_reference","text":"data list charvec(s) charvec data ref charvec reference data method charvec type method used 'exact' used find  identical entries 'ref' data (corrections uppercase'ing) 'grepl' used find entries 'ref' might somehow pre- post- fixed fix_underscores logical flag fix issues underscores data identfiers?","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/fix_typos_with_reference.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Fix typos using reference data — fix_typos_with_reference","text":"list charvec corrected data","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/gDRimport-package.html","id":null,"dir":"Reference","previous_headings":"","what":"gDRimport: Package for handling the import of dose-response data — gDRimport-package","title":"gDRimport: Package for handling the import of dose-response data — gDRimport-package","text":"package part gDR suite. helps prepare raw drug response data downstream processing. mainly contains helper functions importing/loading/validating dose-response data provided different file formats.","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/gDRimport-package.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"gDRimport: Package for handling the import of dose-response data — gDRimport-package","text":"package help page","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/gDRimport-package.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"gDRimport: Package for handling the import of dose-response data — gDRimport-package","text":"learn functions start help(package = \"gDRimport\")","code":""},{"path":[]},{"path":"https://gdrplatform.github.io/gDRimport/reference/gDRimport-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"gDRimport: Package for handling the import of dose-response data — gDRimport-package","text":"Maintainer: Arkadiusz Gladki gladki.arkadiusz@gmail.com (ORCID) Authors: Bartosz Czech (ORCID) Marc Hafner (ORCID) Sergiu Mocanu Dariusz Scigocki Allison Vuong Luca Gerosa (ORCID) Janina Smola","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/gdr_test_data-class.html","id":null,"dir":"Reference","previous_headings":"","what":"gDR Test Data object — gdr_test_data-class","title":"gDR Test Data object — gdr_test_data-class","text":"Object class gdr_test_data build function get_test_data()","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/gdr_test_data-class.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"gDR Test Data object — gdr_test_data-class","text":"object class gdr_test_data primary test data","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/gdr_test_data-class.html","id":"slots","dir":"Reference","previous_headings":"","what":"Slots","title":"gDR Test Data object — gdr_test_data-class","text":"manifest_path character, path manifest file result_path character, path(s) results file template_path character, path(s) data.table template data ref_m_df character, data.table manifest data ref_r1_r2 character, path reference file raw data treated & untreated ref_r1 character, path reference file raw data treated ref_t1_t2 character, path reference template file treated & untreated data ref_t1 character, path reference template file treated data","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/getPSet.html","id":null,"dir":"Reference","previous_headings":"","what":"Get PharmacoSet — getPSet","title":"Get PharmacoSet — getPSet","text":"Get PharmacoSet","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/getPSet.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get PharmacoSet — getPSet","text":"","code":"getPSet(   pset_name,   psetDir = getwd(),   canonical = FALSE,   timeout = 600,   use_local_PSets_list = FALSE )"},{"path":"https://gdrplatform.github.io/gDRimport/reference/getPSet.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get PharmacoSet — getPSet","text":"pset_name string name PharmacoSet psetDir string temporary directory PharmacoSet canonical logical flag indicating PSet canonical timeout maximum number seconds allowed PSet download use_local_PSets_list logical flag PSets list used local. FALSE PSets list taken web.","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/getPSet.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get PharmacoSet — getPSet","text":"PharmacoSet object","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/getPSet.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get PharmacoSet — getPSet","text":"","code":"suppressMessages(getPSet(   \"Tavor_2020\",    psetDir = system.file(\"extdata/pset\", package = \"gDRimport\"),   use_local_PSets_list = TRUE )) #> <PharmacoSet> #> Name:  Tavor  #> Date Created:  Fri Feb  4 17:32:17 2022  #> Number of samples:  53  #> Molecular profiles: #> RNAseq : #>   Dim: 24137, 43  #> Treatment response: #> Drug pertubation: #>    Please look at pertNumber(cSet) to determine number of experiments  for each drug-sample combination. #> Drug sensitivity: #>    Number of Experiments:  2668  #>    Please look at sensNumber(cSet) to determine number of  experiments for each drug-sample combination."},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_EnVision_properties.html","id":null,"dir":"Reference","previous_headings":"","what":"Get properties of EnVision data — get_EnVision_properties","title":"Get properties of EnVision data — get_EnVision_properties","text":"function return properties EnVision data","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_EnVision_properties.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get properties of EnVision data — get_EnVision_properties","text":"","code":"get_EnVision_properties(results.list, fname)"},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_EnVision_properties.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get properties of EnVision data — get_EnVision_properties","text":"results.list list EnVision data fname name input file","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_EnVision_properties.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get properties of EnVision data — get_EnVision_properties","text":"list EnVision propertiesa","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_df_from_raw_edited_EnVision_df.html","id":null,"dir":"Reference","previous_headings":"","what":"Get final results (as a data.table)\nfrom raw edited EnVision data.table — get_df_from_raw_edited_EnVision_df","title":"Get final results (as a data.table)\nfrom raw edited EnVision data.table — get_df_from_raw_edited_EnVision_df","text":"Get final results (data.table) raw edited EnVision data.table","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_df_from_raw_edited_EnVision_df.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get final results (as a data.table)\nfrom raw edited EnVision data.table — get_df_from_raw_edited_EnVision_df","text":"","code":"get_df_from_raw_edited_EnVision_df(   df,   barcode_idx,   barcode_col,   n_row,   n_col,   fname,   sheet_name,   headers )"},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_df_from_raw_edited_EnVision_df.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get final results (as a data.table)\nfrom raw edited EnVision data.table — get_df_from_raw_edited_EnVision_df","text":"df raw data.table barcode_idx numeric vector barcode indices barcode_col column number barcode data n_row number rows n_col number columns fname file name sheet_name name Excel sheet headers list headersa","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_df_from_raw_edited_EnVision_df.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get final results (as a data.table)\nfrom raw edited EnVision data.table — get_df_from_raw_edited_EnVision_df","text":"data.table derived EnVision data","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_df_from_raw_unedited_EnVision_df.html","id":null,"dir":"Reference","previous_headings":"","what":"Get final results (as a data.table)\nfrom raw unedited EnVision data.table — get_df_from_raw_unedited_EnVision_df","title":"Get final results (as a data.table)\nfrom raw unedited EnVision data.table — get_df_from_raw_unedited_EnVision_df","text":"Get final results (data.table) raw unedited EnVision data.table","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_df_from_raw_unedited_EnVision_df.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get final results (as a data.table)\nfrom raw unedited EnVision data.table — get_df_from_raw_unedited_EnVision_df","text":"","code":"get_df_from_raw_unedited_EnVision_df(df, n_row, n_col, barcode_col)"},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_df_from_raw_unedited_EnVision_df.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get final results (as a data.table)\nfrom raw unedited EnVision data.table — get_df_from_raw_unedited_EnVision_df","text":"df raw data.table n_row number rows n_col number columns barcode_col column number barcode data","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_df_from_raw_unedited_EnVision_df.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get final results (as a data.table)\nfrom raw unedited EnVision data.table — get_df_from_raw_unedited_EnVision_df","text":"data.table derived EnVision data","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_excel_sheet_names.html","id":null,"dir":"Reference","previous_headings":"","what":"get Excel sheets names for a charvec of files\nfor non-Excel files return 0 — get_excel_sheet_names","title":"get Excel sheets names for a charvec of files\nfor non-Excel files return 0 — get_excel_sheet_names","text":"get Excel sheets names charvec files non-Excel files return 0","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_excel_sheet_names.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"get Excel sheets names for a charvec of files\nfor non-Excel files return 0 — get_excel_sheet_names","text":"","code":"get_excel_sheet_names(fls)"},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_excel_sheet_names.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"get Excel sheets names for a charvec of files\nfor non-Excel files return 0 — get_excel_sheet_names","text":"fls charvec file pathsa","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_excel_sheet_names.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"get Excel sheets names for a charvec of files\nfor non-Excel files return 0 — get_excel_sheet_names","text":"list one element per file sheet names 0 (non-Excel file)","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_exception_data.html","id":null,"dir":"Reference","previous_headings":"","what":"get exception data — get_exception_data","title":"get exception data — get_exception_data","text":"get exception data","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_exception_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"get exception data — get_exception_data","text":"","code":"get_exception_data(status_code = NULL)"},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_exception_data.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"get exception data — get_exception_data","text":"status_code numeric value","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_exception_data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"get exception data — get_exception_data","text":"data.table row exception data exceptions","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_exception_data.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"get exception data — get_exception_data","text":"","code":"get_exception_data(1) #>    status_code                  title #>         <char>                 <char> #> 1:           1 Error loading manifest #>                                         sprintf_text   type input_type #>                                               <char> <char>     <char> #> 1: There were errors loading manifest. See logs:\\n%s  error   manifest get_exception_data() #>     status_code                                    title #>          <char>                                   <char> #>  1:           1                   Error loading manifest #>  2:           2                       Manifest not found #>  3:           3                  Error loading treatment #>  4:           4                Warning loading treatment #>  5:           5                  Error loading treatment #>  6:           6     Missing data for some Barcode, Plate #>  7:           7     Missing data for some Barcode, Plate #>  8:           8                   Error loading raw data #>  9:           9                   Error loading raw data #> 10:          10                Error during merging data #> 11:          11                  Missing treatment files #> 12:          12                   Error reading Manifest #> 13:          13                     Manifest file format #> 14:          14                        Manifest barcodes #> 15:          15                       Treatment controls #> 16:          16                          Instrument type #> 17:          17                     Treatment sheet name #> 18:          18                     Treatment entry name #> 19:          19                  Error loading treatment #> 20:          20         Error loading specific treatment #> 21:          21          Error reading specific raw data #> 22:          22 Error reading sheet in the raw data file #> 23:          23      Error with readout values in plates #> 24:          24             Error with treatment headers #> 25:          25         Error with treatment file sheets #> 26:          26              Metadata special characters #> 27:          27                         Metadata invalid #> 28:          28                       Raw Data delimiter #> 29:          29                        Raw Data EnVision #> 30:          30                      Raw Data Plate size #> 31:          31                       Raw Data structure #> 32:          32 Treatment File Gnumber and Concentration #> 33:          33                Error loading input files #> 34:          34                  Missing drug annotation #> 35:          35             Missing cell line annotation #> 36:          36                    Invalid averaged data #>     status_code                                    title #>                                                                                                                                                                                                      sprintf_text #>                                                                                                                                                                                                            <char> #>  1:                                                                                                                                                             There were errors loading manifest. See logs:\\n%s #>  2:                                                                                                                                                                                         Please load manifest! #>  3:                                                         Some of the treatment files entered in the manifest have not been uploaded:\\n%s\\nPlease check the uploaded files and their name (including extension) #>  4:                                                                                                                                                                     Some uploaded files (**%s**) are not used #>  5:                                                                                                                                                  There were errors when loading the treatments. See logs:\\n%s #>  6:                                                                                                           Some plates (**%s**) found in the manifest are not reported in the data files and will be discarded #>  7:                                                                                                           Some plates (**%s**) found in the data files are not reported in the manifest and will be discarded #>  8:                                                                                                                         Txt file in an unsupported format. Please check if the file uses tab(\\t) as separator #>  9:                                                                                                                                                        There were errors when loading raw data. See logs:\\n%s #> 10:                                                                                                                                                            There were errors when merging data. See logs:\\n%s #> 11:                                                                                                                                                                          Some treatment files are missing: %s #> 12:                                                                                                                                         There were errors reading the manifest file. Please see the logs:\\n%s #> 13:                                                                                                                         %s file format is not supported. Please convert your file to one of the following: %s #> 14:                                                                                                                                                                          Barcodes in Manifest must be unique! #> 15:                                                                                                                   No untreated controls were found in the treatment. Please upload the appropriate treatment. #> 16:                                                                                                                                                                                  Unrecognized instrument type #> 17:                                                                                                                                                         In untreated treatment file %s, sheet name must be %s #> 18:                                                                                                                                                            In untreated treatment file %s, entries must be %s #> 19:                                                                                                                                             There were errors loading the treatment. Please see the logs:\\n%s #> 20:                                                                                                                                                 There were errors loading treatment %s. Please see logs: \\n%s #> 21:                                                                                                                                                                                              Error reading %s #> 22:                                                                                                                                                                                    Error reading %s, sheet %s #> 23:                                                                                                                                        In result file %s (sheet %s) readout values are misplaced for plate %s #> 24:                                                                    Treatment does not contain all expected headers for a '%s'. '%s' is/are required. Please correct your treatment or change the identifiers. #> 25:                                                                                                                                  Treatment file %s does not contain %s sheets. Please correct your treatment. #> 26:                                                                                                                      Metadata field names for %s cannot contain special characters or start with a number: %s #> 27:                                                                                                                                              Metadata field name: %s in %s is not valid (reserved for output) #> 28:                                                                                                                                                             Can't guess separator for the delimited files: %s #> 29:                                                                                                                                                          Error reading %s: not an original EnVision .csv file #> 30:                                                                                                                                                                            Error reading %s: wrong plate size #> 31:                                                                                                                                       In result file %s (sheet %s) readout values are misplaced for plate %s. #> 32:                           Treatment file(s) %s do/does not contain the same number of Gnumber_* and Concentration_* sheets. Gnumber_* and Concentration_* sheets are required. Please correct your treatment. #> 33:                                                                                         Some input files are missing. Please upload only files with names starting with Manifest_*, Treatment_* and RawData_* #> 34:                                                                                                                 The following drugs IDs are missing: '%s'. <br>Don't worry, drug names will be used for them. #> 35:                                                                                                        The following cell line IDs are missing: '%s'. <br>Don't worry, cell line names will be used for them. #> 36: Averaged dose-response data for the selected cell line and drug: '%s' can be considered invalid. Please check your data in the module 'Manage Data' or contact gdrplatform team via 'gdr-support-d@gene.com'. #>                                                                                                                                                                                                      sprintf_text #>        type   input_type #>      <char>       <char> #>  1:   error     manifest #>  2:   error     manifest #>  3:   error    treatment #>  4: warning    treatment #>  5:   error    treatment #>  6: warning     manifest #>  7: warning     manifest #>  8:   error     raw data #>  9:   error     raw data #> 10:   error merging data #> 11:   error    treatment #> 12:   error     manifest #> 13:   error     manifest #> 14:   error     manifest #> 15:   error    treatment #> 16:   error     raw data #> 17:   error    treatment #> 18:   error    treatment #> 19:   error    treatment #> 20:   error    treatment #> 21:   error     raw data #> 22:   error     raw data #> 23:   error     raw data #> 24:   error    treatment #> 25:   error    treatment #> 26:   error     metadata #> 27:   error     metadata #> 28:   error     raw data #> 29:   error     raw data #> 30:   error     raw data #> 31:   error     raw data #> 32:   error    treatment #> 33:   error  input files #> 34: warning   submit tab #> 35: warning   submit tab #> 36:   error   assay data #>        type   input_type"},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_expected_template_sheets.html","id":null,"dir":"Reference","previous_headings":"","what":"Get names of the sheets expected in templates xlsx — get_expected_template_sheets","title":"Get names of the sheets expected in templates xlsx — get_expected_template_sheets","text":"Get names sheets expected templates xlsx","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_expected_template_sheets.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get names of the sheets expected in templates xlsx — get_expected_template_sheets","text":"","code":"get_expected_template_sheets(type = c(\"all\", \"core\", \"optional\"))"},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_expected_template_sheets.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get names of the sheets expected in templates xlsx — get_expected_template_sheets","text":"type charvec type sheets","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_expected_template_sheets.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get names of the sheets expected in templates xlsx — get_expected_template_sheets","text":"string type sheets","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_plate_info_from_template_xlsx.html","id":null,"dir":"Reference","previous_headings":"","what":"Get plate info from template xlsx — get_plate_info_from_template_xlsx","title":"Get plate info from template xlsx — get_plate_info_from_template_xlsx","text":"Get plate info template xlsx","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_plate_info_from_template_xlsx.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get plate info from template xlsx — get_plate_info_from_template_xlsx","text":"","code":"get_plate_info_from_template_xlsx(template_file, Gnumber_idx, idx)"},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_plate_info_from_template_xlsx.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get plate info from template xlsx — get_plate_info_from_template_xlsx","text":"template_file character, file path(s) template(s) Gnumber_idx index Gnumber data idx template file index","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_plate_info_from_template_xlsx.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get plate info from template xlsx — get_plate_info_from_template_xlsx","text":"list plate info","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_test_D300_data.html","id":null,"dir":"Reference","previous_headings":"","what":"get test D300 data — get_test_D300_data","title":"get test D300 data — get_test_D300_data","text":"get test D300 data","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_test_D300_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"get test D300 data — get_test_D300_data","text":"","code":"get_test_D300_data()"},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_test_D300_data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"get test D300 data — get_test_D300_data","text":"list input data (manifest/template/result paths) related reference data (qs file paths)","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_test_D300_data.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"get test D300 data — get_test_D300_data","text":"","code":"get_test_D300_data() #> $f_96w #> $f_96w$d300 #> [1] \"/usr/local/lib/R/site-library/gDRimport/extdata/data3/D300_96_well_plate_example.tdd\" #>  #> $f_96w$Gnum #> [1] \"/usr/local/lib/R/site-library/gDRimport/extdata/data3/Gnumber_D300_96_well_plate.xlsx\" #>  #> $f_96w$dest_path #> [1] \"/usr/local/lib/R/site-library/gDRimport/extdata/data3/output_files_96w/output\" #>  #> $f_96w$ref_d300 #> [1] \"/usr/local/lib/R/site-library/gDRimport/extdata/data3/ref_D300_96_well_plate_example.qs\" #>  #> $f_96w$ref_Gnum #> [1] \"/usr/local/lib/R/site-library/gDRimport/extdata/data3/ref_Gnumber_D300_96_well_plate.qs\" #>  #> $f_96w$ref_output_path #> [1] \"/usr/local/lib/R/site-library/gDRimport/extdata/data3/output_files_96w/reference\" #>  #>  #> $f_384w #> $f_384w$d300 #> [1] \"/usr/local/lib/R/site-library/gDRimport/extdata/data3/D300_384_well_plate_example.tdd\" #>  #> $f_384w$Gnum #> [1] \"/usr/local/lib/R/site-library/gDRimport/extdata/data3/Gnumber_D300_384_well_plate.xlsx\" #>  #> $f_384w$ref_Gnum #> [1] \"/usr/local/lib/R/site-library/gDRimport/extdata/data3/ref_Gnumber_D300_384_well_plate.qs\" #>  #> $f_384w$ref_d300 #> [1] \"/usr/local/lib/R/site-library/gDRimport/extdata/data3/ref_D300_384_well_plate_example.qs\" #>  #> $f_384w$dest_path #> [1] \"/usr/local/lib/R/site-library/gDRimport/extdata/data3/output_files_384w/output\" #>  #> $f_384w$ref_output_path #> [1] \"/usr/local/lib/R/site-library/gDRimport/extdata/data3/output_files_384w/reference\" #>  #>"},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_test_EnVision_data.html","id":null,"dir":"Reference","previous_headings":"","what":"get test EnVision data — get_test_EnVision_data","title":"get test EnVision data — get_test_EnVision_data","text":"get test EnVision data","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_test_EnVision_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"get test EnVision data — get_test_EnVision_data","text":"","code":"get_test_EnVision_data()"},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_test_EnVision_data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"get test EnVision data — get_test_EnVision_data","text":"list input data (manifest/template/result paths) related reference data (.qs file paths)","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_test_EnVision_data.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"get test EnVision data — get_test_EnVision_data","text":"","code":"get_test_EnVision_data() #> $m_file #> [1] \"/usr/local/lib/R/site-library/gDRimport/extdata/data4/Manifest.xlsx\" #>  #> $r_files #>  [1] \"/usr/local/lib/R/site-library/gDRimport/extdata/data4/H0109269D00.csv\" #>  [2] \"/usr/local/lib/R/site-library/gDRimport/extdata/data4/H0109269D01.csv\" #>  [3] \"/usr/local/lib/R/site-library/gDRimport/extdata/data4/H0309269D00.csv\" #>  [4] \"/usr/local/lib/R/site-library/gDRimport/extdata/data4/H0309269D01.csv\" #>  [5] \"/usr/local/lib/R/site-library/gDRimport/extdata/data4/H0409269D00.csv\" #>  [6] \"/usr/local/lib/R/site-library/gDRimport/extdata/data4/H0409269D01.csv\" #>  [7] \"/usr/local/lib/R/site-library/gDRimport/extdata/data4/H0509269D00.csv\" #>  [8] \"/usr/local/lib/R/site-library/gDRimport/extdata/data4/H0509269D01.csv\" #>  [9] \"/usr/local/lib/R/site-library/gDRimport/extdata/data4/H0609269D00.csv\" #> [10] \"/usr/local/lib/R/site-library/gDRimport/extdata/data4/H0609269D01.csv\" #> [11] \"/usr/local/lib/R/site-library/gDRimport/extdata/data4/H0709269D00.csv\" #> [12] \"/usr/local/lib/R/site-library/gDRimport/extdata/data4/H0709269D01.csv\" #> [13] \"/usr/local/lib/R/site-library/gDRimport/extdata/data4/H0809269D00.csv\" #> [14] \"/usr/local/lib/R/site-library/gDRimport/extdata/data4/H0809269D01.csv\" #> [15] \"/usr/local/lib/R/site-library/gDRimport/extdata/data4/H0909269D00.csv\" #> [16] \"/usr/local/lib/R/site-library/gDRimport/extdata/data4/H0909269D01.csv\" #> [17] \"/usr/local/lib/R/site-library/gDRimport/extdata/data4/H1109269D00.csv\" #> [18] \"/usr/local/lib/R/site-library/gDRimport/extdata/data4/H1109269D01.csv\" #> [19] \"/usr/local/lib/R/site-library/gDRimport/extdata/data4/H1209269D00.csv\" #> [20] \"/usr/local/lib/R/site-library/gDRimport/extdata/data4/H1209269D01.csv\" #> [21] \"/usr/local/lib/R/site-library/gDRimport/extdata/data4/H1409269D00.csv\" #> [22] \"/usr/local/lib/R/site-library/gDRimport/extdata/data4/H1409269D01.csv\" #> [23] \"/usr/local/lib/R/site-library/gDRimport/extdata/data4/K0209269D00.csv\" #> [24] \"/usr/local/lib/R/site-library/gDRimport/extdata/data4/K0209269D01.csv\" #> [25] \"/usr/local/lib/R/site-library/gDRimport/extdata/data4/K0809269D00.csv\" #> [26] \"/usr/local/lib/R/site-library/gDRimport/extdata/data4/K0809269D01.csv\" #> [27] \"/usr/local/lib/R/site-library/gDRimport/extdata/data4/K1009269D00.csv\" #> [28] \"/usr/local/lib/R/site-library/gDRimport/extdata/data4/K1009269D01.csv\" #>  #> $t_files #> [1] \"/usr/local/lib/R/site-library/gDRimport/extdata/data4/Project40.treated.template.xlsx\"   #> [2] \"/usr/local/lib/R/site-library/gDRimport/extdata/data4/Project40.untreated.template.xlsx\" #>  #> $ref_l_path #> [1] \"/usr/local/lib/R/site-library/gDRimport/extdata/data4/ref_l.qs\" #>"},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_test_Tecan_data.html","id":null,"dir":"Reference","previous_headings":"","what":"get test Tecan data — get_test_Tecan_data","title":"get test Tecan data — get_test_Tecan_data","text":"get test Tecan data","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_test_Tecan_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"get test Tecan data — get_test_Tecan_data","text":"","code":"get_test_Tecan_data()"},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_test_Tecan_data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"get test Tecan data — get_test_Tecan_data","text":"list input data (manifest/template/result paths) related reference data (qs file paths)","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_test_Tecan_data.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"get test Tecan data — get_test_Tecan_data","text":"","code":"get_test_Tecan_data() #> $m_file #> [1] \"/usr/local/lib/R/site-library/gDRimport/extdata/data2/manifest_Tecan_96_well_plates.xlsx\" #>  #> $r_files #> [1] \"/usr/local/lib/R/site-library/gDRimport/extdata/data2/RawData_Tecan_96_well_plates.xlsx\" #>  #> $t_files #> [1] \"/usr/local/lib/R/site-library/gDRimport/extdata/data2/D300_trt_Tecan_96_well_plates.xlsx\" #>  #> $ref_m_df #> [1] \"/usr/local/lib/R/site-library/gDRimport/extdata/data2/ref_manifest_Tecan_96_well_plates.qs\" #>  #> $ref_r_df #> [1] \"/usr/local/lib/R/site-library/gDRimport/extdata/data2/ref_RawData_Tecan_96_well_plates.qs\" #>  #> $ref_t_df #> [1] \"/usr/local/lib/R/site-library/gDRimport/extdata/data2/ref_D300_trt_Tecan_96_well_plates.qs\" #>"},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_test_data.html","id":null,"dir":"Reference","previous_headings":"","what":"get primary test data — get_test_data","title":"get primary test data — get_test_data","text":"get primary test data","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_test_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"get primary test data — get_test_data","text":"","code":"get_test_data()"},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_test_data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"get primary test data — get_test_data","text":"object class \"gdr_test_data\" input data (manifest/template/result paths) related reference data (qs file paths)","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_test_data.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"get primary test data — get_test_data","text":"","code":"get_test_data() #> class: gdr_test_data  #> slots: manifest_path result_path template_path ref_m_df ref_r1_r2 ref_r1 ref_t1_t2 ref_t1"},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_test_tsv_data.html","id":null,"dir":"Reference","previous_headings":"","what":"get test tsv data — get_test_tsv_data","title":"get test tsv data — get_test_tsv_data","text":"get test tsv data","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_test_tsv_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"get test tsv data — get_test_tsv_data","text":"","code":"get_test_tsv_data()"},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_test_tsv_data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"get test tsv data — get_test_tsv_data","text":"list input data (manifest/template/result paths) related reference data (.qs file paths)","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_test_tsv_data.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"get test tsv data — get_test_tsv_data","text":"","code":"get_test_tsv_data() #> $m_file #> [1] \"/usr/local/lib/R/site-library/gDRimport/extdata/data5/Manifest.tsv\" #>  #> $r_files #> [1] \"/usr/local/lib/R/site-library/gDRimport/extdata/data5/RawData.tsv\" #>  #> $t_files #> [1] \"/usr/local/lib/R/site-library/gDRimport/extdata/data5/Template_trt.tsv\"   #> [2] \"/usr/local/lib/R/site-library/gDRimport/extdata/data5/Template_untrt.tsv\" #>  #> $ref_l_path #> [1] \"/usr/local/lib/R/site-library/gDRimport/extdata/data5/ref_l.qs\" #>"},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_xl_sheets.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Excel sheets — get_xl_sheets","title":"Get Excel sheets — get_xl_sheets","text":"get sheets given set XLS files","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_xl_sheets.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Excel sheets — get_xl_sheets","text":"","code":"get_xl_sheets(files)"},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_xl_sheets.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Excel sheets — get_xl_sheets","text":"files charvec file paths","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_xl_sheets.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Excel sheets — get_xl_sheets","text":"named list names excel filenames values sheets within file","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/import_D300.html","id":null,"dir":"Reference","previous_headings":"","what":"Import D300 — import_D300","title":"Import D300 — import_D300","text":"functions takes D300 file generates corresponding template files","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/import_D300.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Import D300 — import_D300","text":"","code":"import_D300(D300_file, metadata_file, destination_path)"},{"path":"https://gdrplatform.github.io/gDRimport/reference/import_D300.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Import D300 — import_D300","text":"D300_file character, file path D300 file metadata_file character, file path file mapping D300 names Gnumbers destination_path character, path folder template files generated","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/import_D300.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Import D300 — import_D300","text":"Create one Excel file per plate. sheet plate file describes drugs corrresponding concentrations tested well.","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/import_D300.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Import D300 — import_D300","text":"example, wells treated 2 drugs combination result 4 sheets per plate. Sheet 1: Drug 1 Sheet 2: Conc Drug 1 Sheet 3: Drug 2 Sheet 4: Conc Drug 2","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/import_D300.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Import D300 — import_D300","text":"","code":"td3 <- get_test_D300_data()[[\"f_96w\"]] o_path <- file.path(tempdir(), \"td3\") dir.create(o_path) import_D300(td3$d300, td3$Gnum, o_path) list.files(o_path) #>  [1] \"trt_P1.xlsx\"  \"trt_P10.xlsx\" \"trt_P11.xlsx\" \"trt_P12.xlsx\" \"trt_P13.xlsx\" #>  [6] \"trt_P14.xlsx\" \"trt_P15.xlsx\" \"trt_P16.xlsx\" \"trt_P17.xlsx\" \"trt_P18.xlsx\" #> [11] \"trt_P19.xlsx\" \"trt_P2.xlsx\"  \"trt_P20.xlsx\" \"trt_P21.xlsx\" \"trt_P22.xlsx\" #> [16] \"trt_P3.xlsx\"  \"trt_P4.xlsx\"  \"trt_P5.xlsx\"  \"trt_P6.xlsx\"  \"trt_P7.xlsx\"  #> [21] \"trt_P8.xlsx\"  \"trt_P9.xlsx\"  unlink(o_path, recursive = TRUE)"},{"path":"https://gdrplatform.github.io/gDRimport/reference/is_readable_v.html","id":null,"dir":"Reference","previous_headings":"","what":"is_readable_v\nCheck if all paths in vector are readable — is_readable_v","title":"is_readable_v\nCheck if all paths in vector are readable — is_readable_v","text":"is_readable_v Check paths vector readable","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/is_readable_v.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"is_readable_v\nCheck if all paths in vector are readable — is_readable_v","text":"","code":"is_readable_v(paths)"},{"path":"https://gdrplatform.github.io/gDRimport/reference/is_readable_v.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"is_readable_v\nCheck if all paths in vector are readable — is_readable_v","text":"paths character path(s)","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/is_readable_v.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"is_readable_v\nCheck if all paths in vector are readable — is_readable_v","text":"NULL invisibly.","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/is_readable_v.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"is_readable_v\nCheck if all paths in vector are readable — is_readable_v","text":"","code":"td2 <- get_test_Tecan_data() is_readable_v(td2$r_files) #> [1] TRUE"},{"path":"https://gdrplatform.github.io/gDRimport/reference/load_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Load data — load_data","title":"Load data — load_data","text":"functions loads checks data file(s)","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/load_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Load data — load_data","text":"","code":"load_data(   manifest_file,   df_template_files,   results_file,   instrument = \"EnVision\" )"},{"path":"https://gdrplatform.github.io/gDRimport/reference/load_data.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Load data — load_data","text":"manifest_file character, file path(s) manifest(s) df_template_files data.table, datapaths names results file(s) character file path templates file(s) results_file data.table, datapaths names results file(s) character file path results file(s) instrument character","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/load_data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Load data — load_data","text":"list three data.tables manifest/treatment results","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/load_data.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Load data — load_data","text":"","code":"td <- get_test_data()  l_tbl <- load_data(manifest_path(td), template_path(td), result_path(td)) #> INFO [2024-11-07 10:36:50] Manifest loaded successfully #> INFO [2024-11-07 10:36:50] Reading Template_7daytreated.xlsx with load_templates_xlsx #> INFO [2024-11-07 10:36:50] Loading Template_7daytreated.xlsx #> INFO [2024-11-07 10:36:50] Loading Template_Untreated.xlsx #> INFO [2024-11-07 10:36:50] Templates loaded successfully! #> INFO [2024-11-07 10:36:50] Reading file /usr/local/lib/R/site-library/gDRimport/extdata/data1/RawData_day0.xlsx, sheet Readout_0077vs0068_day7 #> New names: #> • `` -> `...1` #> • `` -> `...2` #> • `` -> `...3` #> • `` -> `...4` #> • `` -> `...5` #> • `` -> `...6` #> • `` -> `...7` #> • `` -> `...8` #> • `` -> `...9` #> • `` -> `...10` #> • `` -> `...11` #> • `` -> `...12` #> • `` -> `...13` #> • `` -> `...14` #> • `` -> `...15` #> • `` -> `...16` #> • `` -> `...17` #> • `` -> `...18` #> • `` -> `...19` #> • `` -> `...20` #> • `` -> `...21` #> • `` -> `...22` #> • `` -> `...23` #> • `` -> `...24` #> • `` -> `...25` #> INFO [2024-11-07 10:36:50] Plate 201904190a read; 384 wells #> INFO [2024-11-07 10:36:50] Plate 201904190b read; 384 wells #> INFO [2024-11-07 10:36:50] Plate 201904190c read; 384 wells #> INFO [2024-11-07 10:36:50] Plate 201904190d read; 384 wells #> INFO [2024-11-07 10:36:50] Plate 201904190e read; 384 wells #> INFO [2024-11-07 10:36:50] Plate 201904190f read; 384 wells #> INFO [2024-11-07 10:36:50] File done #> INFO [2024-11-07 10:36:50] Reading file /usr/local/lib/R/site-library/gDRimport/extdata/data1/RawData_day7.xlsx, sheet Readout_0077vs0068_day7 #> New names: #> • `` -> `...1` #> • `` -> `...2` #> • `` -> `...3` #> • `` -> `...4` #> • `` -> `...5` #> • `` -> `...6` #> • `` -> `...7` #> • `` -> `...8` #> • `` -> `...9` #> • `` -> `...10` #> • `` -> `...11` #> • `` -> `...12` #> • `` -> `...13` #> • `` -> `...14` #> • `` -> `...15` #> • `` -> `...16` #> • `` -> `...17` #> • `` -> `...18` #> • `` -> `...19` #> • `` -> `...20` #> • `` -> `...21` #> • `` -> `...22` #> • `` -> `...23` #> • `` -> `...24` #> • `` -> `...25` #> INFO [2024-11-07 10:36:51] Plate 201904197a read; 384 wells #> INFO [2024-11-07 10:36:51] Plate 201904197b read; 384 wells #> INFO [2024-11-07 10:36:51] Plate 201904197c read; 384 wells #> INFO [2024-11-07 10:36:51] Plate 201904197d read; 384 wells #> INFO [2024-11-07 10:36:51] Plate 201904197e read; 384 wells #> INFO [2024-11-07 10:36:51] Plate 201904197f read; 384 wells #> INFO [2024-11-07 10:36:51] File done"},{"path":"https://gdrplatform.github.io/gDRimport/reference/load_manifest.html","id":null,"dir":"Reference","previous_headings":"","what":"Load manifest — load_manifest","title":"Load manifest — load_manifest","text":"functions loads checks manifest file(s)","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/load_manifest.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Load manifest — load_manifest","text":"","code":"load_manifest(manifest_file)"},{"path":"https://gdrplatform.github.io/gDRimport/reference/load_manifest.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Load manifest — load_manifest","text":"manifest_file character, file path(s) manifest(s)","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/load_manifest.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Load manifest — load_manifest","text":"list manifest data.table headers","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/load_manifest.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Load manifest — load_manifest","text":"","code":"td <- get_test_data()  ml <- load_manifest(manifest_path(td)) #> INFO [2024-11-07 10:36:51] Manifest loaded successfully"},{"path":"https://gdrplatform.github.io/gDRimport/reference/load_results.html","id":null,"dir":"Reference","previous_headings":"","what":"Load results — load_results","title":"Load results — load_results","text":"functions loads checks results file(s)","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/load_results.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Load results — load_results","text":"","code":"load_results(   df_results_files,   instrument = \"EnVision\",   headers = gDRutils::get_env_identifiers() )"},{"path":"https://gdrplatform.github.io/gDRimport/reference/load_results.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Load results — load_results","text":"df_results_files data.table, datapaths names results file(s) character file path results file(s) instrument character headers list headers identified manifest file","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/load_results.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Load results — load_results","text":"data.table results' data","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/load_results.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Load results — load_results","text":"","code":"td <- get_test_data()  r_df <- load_results(result_path(td)) #> INFO [2024-11-07 10:36:51] Reading file /usr/local/lib/R/site-library/gDRimport/extdata/data1/RawData_day0.xlsx, sheet Readout_0077vs0068_day7 #> New names: #> • `` -> `...1` #> • `` -> `...2` #> • `` -> `...3` #> • `` -> `...4` #> • `` -> `...5` #> • `` -> `...6` #> • `` -> `...7` #> • `` -> `...8` #> • `` -> `...9` #> • `` -> `...10` #> • `` -> `...11` #> • `` -> `...12` #> • `` -> `...13` #> • `` -> `...14` #> • `` -> `...15` #> • `` -> `...16` #> • `` -> `...17` #> • `` -> `...18` #> • `` -> `...19` #> • `` -> `...20` #> • `` -> `...21` #> • `` -> `...22` #> • `` -> `...23` #> • `` -> `...24` #> • `` -> `...25` #> INFO [2024-11-07 10:36:51] Plate 1 read; 384 wells #> INFO [2024-11-07 10:36:51] Plate 2 read; 384 wells #> INFO [2024-11-07 10:36:51] Plate 3 read; 384 wells #> INFO [2024-11-07 10:36:51] Plate 4 read; 384 wells #> INFO [2024-11-07 10:36:51] Plate 5 read; 384 wells #> INFO [2024-11-07 10:36:51] Plate 6 read; 384 wells #> INFO [2024-11-07 10:36:51] File done #> INFO [2024-11-07 10:36:51] Reading file /usr/local/lib/R/site-library/gDRimport/extdata/data1/RawData_day7.xlsx, sheet Readout_0077vs0068_day7 #> New names: #> • `` -> `...1` #> • `` -> `...2` #> • `` -> `...3` #> • `` -> `...4` #> • `` -> `...5` #> • `` -> `...6` #> • `` -> `...7` #> • `` -> `...8` #> • `` -> `...9` #> • `` -> `...10` #> • `` -> `...11` #> • `` -> `...12` #> • `` -> `...13` #> • `` -> `...14` #> • `` -> `...15` #> • `` -> `...16` #> • `` -> `...17` #> • `` -> `...18` #> • `` -> `...19` #> • `` -> `...20` #> • `` -> `...21` #> • `` -> `...22` #> • `` -> `...23` #> • `` -> `...24` #> • `` -> `...25` #> INFO [2024-11-07 10:36:51] Plate 1 read; 384 wells #> INFO [2024-11-07 10:36:51] Plate 2 read; 384 wells #> INFO [2024-11-07 10:36:51] Plate 3 read; 384 wells #> INFO [2024-11-07 10:36:51] Plate 4 read; 384 wells #> INFO [2024-11-07 10:36:51] Plate 5 read; 384 wells #> INFO [2024-11-07 10:36:51] Plate 6 read; 384 wells #> INFO [2024-11-07 10:36:51] File done"},{"path":"https://gdrplatform.github.io/gDRimport/reference/load_results_EnVision.html","id":null,"dir":"Reference","previous_headings":"","what":"Load EnVision results from xlsx — load_results_EnVision","title":"Load EnVision results from xlsx — load_results_EnVision","text":"functions loads checks results file(s)","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/load_results_EnVision.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Load EnVision results from xlsx — load_results_EnVision","text":"","code":"load_results_EnVision(results_file, headers = gDRutils::get_env_identifiers())"},{"path":"https://gdrplatform.github.io/gDRimport/reference/load_results_EnVision.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Load EnVision results from xlsx — load_results_EnVision","text":"results_file character vector containing file path(s) results file(s) headers list headers identified manifest","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/load_results_EnVision.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Load EnVision results from xlsx — load_results_EnVision","text":"data.table results data","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/load_results_Tecan.html","id":null,"dir":"Reference","previous_headings":"","what":"Load tecan results from xlsx — load_results_Tecan","title":"Load tecan results from xlsx — load_results_Tecan","text":"functions loads checks results file","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/load_results_Tecan.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Load tecan results from xlsx — load_results_Tecan","text":"","code":"load_results_Tecan(results_file, headers = gDRutils::get_env_identifiers())"},{"path":"https://gdrplatform.github.io/gDRimport/reference/load_results_Tecan.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Load tecan results from xlsx — load_results_Tecan","text":"results_file string, file path result file headers list headers identified manifest","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/load_results_Tecan.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Load tecan results from xlsx — load_results_Tecan","text":"data.table derived Tecan data","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/load_results_tsv.html","id":null,"dir":"Reference","previous_headings":"","what":"Load results from tsv — load_results_tsv","title":"Load results from tsv — load_results_tsv","text":"functions loads checks results file(s)","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/load_results_tsv.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Load results from tsv — load_results_tsv","text":"","code":"load_results_tsv(results_file, headers)"},{"path":"https://gdrplatform.github.io/gDRimport/reference/load_results_tsv.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Load results from tsv — load_results_tsv","text":"results_file character, file path(s) template(s) headers list headers identified manifest","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/load_results_tsv.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Load results from tsv — load_results_tsv","text":"data.table results data","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/load_templates.html","id":null,"dir":"Reference","previous_headings":"","what":"Load templates — load_templates","title":"Load templates — load_templates","text":"functions loads checks template file(s)","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/load_templates.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Load templates — load_templates","text":"","code":"load_templates(df_template_files)"},{"path":"https://gdrplatform.github.io/gDRimport/reference/load_templates.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Load templates — load_templates","text":"df_template_files data.table, datapaths names results file(s) character file path templates file(s)","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/load_templates.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Load templates — load_templates","text":"data.table templates data","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/load_templates.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Load templates — load_templates","text":"","code":"td <- get_test_data()  t_df <- load_templates(template_path(td)) #> INFO [2024-11-07 10:36:52] Reading Template_7daytreated.xlsx with load_templates_xlsx #> INFO [2024-11-07 10:36:52] Loading Template_7daytreated.xlsx #> INFO [2024-11-07 10:36:52] Loading Template_Untreated.xlsx #> INFO [2024-11-07 10:36:52] Templates loaded successfully!"},{"path":"https://gdrplatform.github.io/gDRimport/reference/load_templates_tsv.html","id":null,"dir":"Reference","previous_headings":"","what":"Load templates from tsv — load_templates_tsv","title":"Load templates from tsv — load_templates_tsv","text":"functions loads checks template file(s)","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/load_templates_tsv.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Load templates from tsv — load_templates_tsv","text":"","code":"load_templates_tsv(template_file, template_filename = NULL)"},{"path":"https://gdrplatform.github.io/gDRimport/reference/load_templates_tsv.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Load templates from tsv — load_templates_tsv","text":"template_file character, file path(s) template(s) template_filename character, file name(s)","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/load_templates_tsv.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Load templates from tsv — load_templates_tsv","text":"data.table template data","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/load_templates_xlsx.html","id":null,"dir":"Reference","previous_headings":"","what":"Load templates from xlsx — load_templates_xlsx","title":"Load templates from xlsx — load_templates_xlsx","text":"functions loads checks template file(s)","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/load_templates_xlsx.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Load templates from xlsx — load_templates_xlsx","text":"","code":"load_templates_xlsx(template_file, template_filename = NULL)"},{"path":"https://gdrplatform.github.io/gDRimport/reference/load_templates_xlsx.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Load templates from xlsx — load_templates_xlsx","text":"template_file character, file path(s) template(s) template_filename character, file name(s)","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/load_templates_xlsx.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Load templates from xlsx — load_templates_xlsx","text":"data.table templates data","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/manifest_path-method.html","id":null,"dir":"Reference","previous_headings":"","what":"Method manifest_path — manifest_path","title":"Method manifest_path — manifest_path","text":"Method object gdr_test_data - access slot manifest_path","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/manifest_path-method.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Method manifest_path — manifest_path","text":"","code":"manifest_path(x)  # S4 method for gdr_test_data manifest_path(x)"},{"path":"https://gdrplatform.github.io/gDRimport/reference/manifest_path-method.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Method manifest_path — manifest_path","text":"x object class gdr_test_data","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/manifest_path-method.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Method manifest_path — manifest_path","text":"value slot manifest_path","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/manifest_path-method.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Method manifest_path — manifest_path","text":"","code":"td <- get_test_data()  manifest_file_path <- manifest_path(td)"},{"path":"https://gdrplatform.github.io/gDRimport/reference/mgrepl.html","id":null,"dir":"Reference","previous_headings":"","what":"grep wrapper to support multiple patterns — mgrepl","title":"grep wrapper to support multiple patterns — mgrepl","text":"grep wrapper support multiple patterns","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/mgrepl.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"grep wrapper to support multiple patterns — mgrepl","text":"","code":"mgrepl(patterns, x, do_unlist = TRUE, ...)"},{"path":"https://gdrplatform.github.io/gDRimport/reference/mgrepl.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"grep wrapper to support multiple patterns — mgrepl","text":"patterns charvec patterns checked x charvec data do_unlist logical_flag unlist final results? ... additional argument","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/mgrepl.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"grep wrapper to support multiple patterns — mgrepl","text":"list charvec grep output","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/parse_D300_xml.html","id":null,"dir":"Reference","previous_headings":"","what":"Parse D300 — parse_D300_xml","title":"Parse D300 — parse_D300_xml","text":"function parses D300 *.tdd file (XML format) data.table","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/parse_D300_xml.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Parse D300 — parse_D300_xml","text":"","code":"parse_D300_xml(D300_file)"},{"path":"https://gdrplatform.github.io/gDRimport/reference/parse_D300_xml.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Parse D300 — parse_D300_xml","text":"D300_file string, file path D300 .tdd file","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/parse_D300_xml.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Parse D300 — parse_D300_xml","text":"data.table representing input D300_file.","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/parse_D300_xml.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Parse D300 — parse_D300_xml","text":"","code":"td3 <- get_test_D300_data() fs <- td3[[\"f_96w\"]] dose_df <- parse_D300_xml(fs[[\"d300\"]])"},{"path":"https://gdrplatform.github.io/gDRimport/reference/read_EnVision_delim.html","id":null,"dir":"Reference","previous_headings":"","what":"Read EnVision delimited text files — read_EnVision_delim","title":"Read EnVision delimited text files — read_EnVision_delim","text":"function reads file EnVision Workstation","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/read_EnVision_delim.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read EnVision delimited text files — read_EnVision_delim","text":"","code":"read_EnVision_delim(file, nrows = 10000, seps = c(\",\", \"\\t\"))"},{"path":"https://gdrplatform.github.io/gDRimport/reference/read_EnVision_delim.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read EnVision delimited text files — read_EnVision_delim","text":"file string path input file EnVision scanner nrows maximum number file rows processed seps potential field separators input file","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/read_EnVision_delim.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Read EnVision delimited text files — read_EnVision_delim","text":"list containing data table, n_col, n_row, edited","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/read_EnVision_xlsx.html","id":null,"dir":"Reference","previous_headings":"","what":"Read in single xlsx data from EnVision — read_EnVision_xlsx","title":"Read in single xlsx data from EnVision — read_EnVision_xlsx","text":"Read single xlsx data EnVision","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/read_EnVision_xlsx.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read in single xlsx data from EnVision — read_EnVision_xlsx","text":"","code":"read_EnVision_xlsx(results_file, results_sheet)"},{"path":"https://gdrplatform.github.io/gDRimport/reference/read_EnVision_xlsx.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read in single xlsx data from EnVision — read_EnVision_xlsx","text":"results_file character, file path(s) results file(s) results_sheet results sheet names","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/read_EnVision_xlsx.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Read in single xlsx data from EnVision — read_EnVision_xlsx","text":"data.table results data","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/read_excel_to_dt.html","id":null,"dir":"Reference","previous_headings":"","what":"Read excel file and transorm it into data.table object — read_excel_to_dt","title":"Read excel file and transorm it into data.table object — read_excel_to_dt","text":"Read excel file transorm data.table object","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/read_excel_to_dt.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read excel file and transorm it into data.table object — read_excel_to_dt","text":"","code":"read_excel_to_dt(path, ...)"},{"path":"https://gdrplatform.github.io/gDRimport/reference/read_excel_to_dt.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read excel file and transorm it into data.table object — read_excel_to_dt","text":"path path excel file ... arguments passed readxl::read_excel","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/read_excel_to_dt.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Read excel file and transorm it into data.table object — read_excel_to_dt","text":"data.table object read excel file","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/read_excel_to_dt.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Read excel file and transorm it into data.table object — read_excel_to_dt","text":"","code":"datasets <- readxl::readxl_example(\"datasets.xlsx\") read_excel_to_dt(datasets) #>      Sepal.Length Sepal.Width Petal.Length Petal.Width   Species #>             <num>       <num>        <num>       <num>    <char> #>   1:          5.1         3.5          1.4         0.2    setosa #>   2:          4.9         3.0          1.4         0.2    setosa #>   3:          4.7         3.2          1.3         0.2    setosa #>   4:          4.6         3.1          1.5         0.2    setosa #>   5:          5.0         3.6          1.4         0.2    setosa #>  ---                                                             #> 146:          6.7         3.0          5.2         2.3 virginica #> 147:          6.3         2.5          5.0         1.9 virginica #> 148:          6.5         3.0          5.2         2.0 virginica #> 149:          6.2         3.4          5.4         2.3 virginica #> 150:          5.9         3.0          5.1         1.8 virginica"},{"path":"https://gdrplatform.github.io/gDRimport/reference/read_in_EnVision_file.html","id":null,"dir":"Reference","previous_headings":"","what":"Read EnVision file — read_in_EnVision_file","title":"Read EnVision file — read_in_EnVision_file","text":"function reads file EnVision Workstation","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/read_in_EnVision_file.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read EnVision file — read_in_EnVision_file","text":"","code":"read_in_EnVision_file(file, nrows, seps)"},{"path":"https://gdrplatform.github.io/gDRimport/reference/read_in_EnVision_file.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read EnVision file — read_in_EnVision_file","text":"file input file EnVision nrows maximum number file rows processed seps potential field separators input file","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/read_in_EnVision_file.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Read EnVision file — read_in_EnVision_file","text":"list one element per EnVisoin input file","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/read_in_manifest_file.html","id":null,"dir":"Reference","previous_headings":"","what":"read manifest files — read_in_manifest_file","title":"read manifest files — read_in_manifest_file","text":"read manifest files","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/read_in_manifest_file.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"read manifest files — read_in_manifest_file","text":"","code":"read_in_manifest_file(manifest_file, available_formats)"},{"path":"https://gdrplatform.github.io/gDRimport/reference/read_in_manifest_file.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"read manifest files — read_in_manifest_file","text":"manifest_file character, file path(s) manifest(s) available_formats charvec available file formats","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/read_in_manifest_file.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"read manifest files — read_in_manifest_file","text":"data.table manifest data","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/read_in_result_files.html","id":null,"dir":"Reference","previous_headings":"","what":"Read in results files — read_in_result_files","title":"Read in results files — read_in_result_files","text":"Read results files","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/read_in_result_files.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read in results files — read_in_result_files","text":"","code":"read_in_result_files(results_file, results_filename, headers)"},{"path":"https://gdrplatform.github.io/gDRimport/reference/read_in_result_files.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read in results files — read_in_result_files","text":"results_file data.table, datapaths names results file(s) character file path results file(s) results_filename charvect file names headers list headers identified result files","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/read_in_result_files.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Read in results files — read_in_result_files","text":"data.table results data","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/read_in_results_Tecan.html","id":null,"dir":"Reference","previous_headings":"","what":"read in Tecan data — read_in_results_Tecan","title":"read in Tecan data — read_in_results_Tecan","text":"read Tecan data","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/read_in_results_Tecan.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"read in Tecan data — read_in_results_Tecan","text":"","code":"read_in_results_Tecan(results_file, results_sheets, headers)"},{"path":"https://gdrplatform.github.io/gDRimport/reference/read_in_results_Tecan.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"read in Tecan data — read_in_results_Tecan","text":"results_file string, file path result file results_sheets template sheet names headers list headers identified manifest","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/read_in_results_Tecan.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"read in Tecan data — read_in_results_Tecan","text":"data.table derived Tecan data","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/read_in_template_sheet_xlsx.html","id":null,"dir":"Reference","previous_headings":"","what":"Read in data from xlsx template sheet — read_in_template_sheet_xlsx","title":"Read in data from xlsx template sheet — read_in_template_sheet_xlsx","text":"Read data xlsx template sheet","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/read_in_template_sheet_xlsx.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read in data from xlsx template sheet — read_in_template_sheet_xlsx","text":"","code":"read_in_template_sheet_xlsx(template_file, template_sheets, idx, plate_info)"},{"path":"https://gdrplatform.github.io/gDRimport/reference/read_in_template_sheet_xlsx.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read in data from xlsx template sheet — read_in_template_sheet_xlsx","text":"template_file character, file path(s) template(s) template_sheets template sheet names idx template file index plate_info list plate info","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/read_in_template_sheet_xlsx.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Read in data from xlsx template sheet — read_in_template_sheet_xlsx","text":"data.table template data","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/read_in_template_xlsx.html","id":null,"dir":"Reference","previous_headings":"","what":"Read in xlsx template files — read_in_template_xlsx","title":"Read in xlsx template files — read_in_template_xlsx","text":"Read xlsx template files","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/read_in_template_xlsx.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read in xlsx template files — read_in_template_xlsx","text":"","code":"read_in_template_xlsx(template_file, template_filename, template_sheets)"},{"path":"https://gdrplatform.github.io/gDRimport/reference/read_in_template_xlsx.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read in xlsx template files — read_in_template_xlsx","text":"template_file character, file path(s) template(s) template_filename character, file name(s) template_sheets template sheet names","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/read_in_template_xlsx.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Read in xlsx template files — read_in_template_xlsx","text":"data.table templates data","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/read_in_tsv_template_files.html","id":null,"dir":"Reference","previous_headings":"","what":"read in tsv template files — read_in_tsv_template_files","title":"read in tsv template files — read_in_tsv_template_files","text":"read tsv template files","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/read_in_tsv_template_files.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"read in tsv template files — read_in_tsv_template_files","text":"","code":"read_in_tsv_template_files(template_file, template_filename, templates)"},{"path":"https://gdrplatform.github.io/gDRimport/reference/read_in_tsv_template_files.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"read in tsv template files — read_in_tsv_template_files","text":"template_file character, file path(s) template(s) template_filename character, file name(s) templates list templates data","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/read_in_tsv_template_files.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"read in tsv template files — read_in_tsv_template_files","text":"data.table templates data","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/read_ref_data.html","id":null,"dir":"Reference","previous_headings":"","what":"read_ref_data — read_ref_data","title":"read_ref_data — read_ref_data","text":"Read reference data","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/read_ref_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"read_ref_data — read_ref_data","text":"","code":"read_ref_data(inDir, prefix = \"ref\")"},{"path":"https://gdrplatform.github.io/gDRimport/reference/read_ref_data.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"read_ref_data — read_ref_data","text":"inDir directory path reference data prefix prefix reference file names ('ref' default)","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/read_ref_data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"read_ref_data — read_ref_data","text":"list reference data","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/result_path-method.html","id":null,"dir":"Reference","previous_headings":"","what":"Method result_path — result_path","title":"Method result_path — result_path","text":"Method object gdr_test_data - access slot result_path","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/result_path-method.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Method result_path — result_path","text":"","code":"result_path(x)  # S4 method for gdr_test_data result_path(x)"},{"path":"https://gdrplatform.github.io/gDRimport/reference/result_path-method.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Method result_path — result_path","text":"x object class gdr_test_data","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/result_path-method.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Method result_path — result_path","text":"value slot result_path","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/result_path-method.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Method result_path — result_path","text":"","code":"td <- get_test_data()  result_file_path <- result_path(td)"},{"path":"https://gdrplatform.github.io/gDRimport/reference/save_drug_info_per_well.html","id":null,"dir":"Reference","previous_headings":"","what":"for each drug create a Gnumber and Concentration information for each well — save_drug_info_per_well","title":"for each drug create a Gnumber and Concentration information for each well — save_drug_info_per_well","text":"drug create Gnumber Concentration information well","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/save_drug_info_per_well.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"for each drug create a Gnumber and Concentration information for each well — save_drug_info_per_well","text":"","code":"save_drug_info_per_well(trt_info, trt_gnumber_conc, wb, idfs)"},{"path":"https://gdrplatform.github.io/gDRimport/reference/save_drug_info_per_well.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"for each drug create a Gnumber and Concentration information for each well — save_drug_info_per_well","text":"trt_info list treatment info trt_gnumber_conc list treatment data wb pointer xlsx workbook idfs charvec identifiers","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/save_drug_info_per_well.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"for each drug create a Gnumber and Concentration information for each well — save_drug_info_per_well","text":"NULL invisibly.","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/setEnvForPSet.html","id":null,"dir":"Reference","previous_headings":"","what":"Adjust environment variables to meet gDR standards — setEnvForPSet","title":"Adjust environment variables to meet gDR standards — setEnvForPSet","text":"Adjust environment variables meet gDR standards","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/setEnvForPSet.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Adjust environment variables to meet gDR standards — setEnvForPSet","text":"","code":"setEnvForPSet()"},{"path":"https://gdrplatform.github.io/gDRimport/reference/setEnvForPSet.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Adjust environment variables to meet gDR standards — setEnvForPSet","text":"NULL","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/setEnvForPSet.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Adjust environment variables to meet gDR standards — setEnvForPSet","text":"","code":"setEnvForPSet() gDRutils::reset_env_identifiers()"},{"path":"https://gdrplatform.github.io/gDRimport/reference/standardize_record_values.html","id":null,"dir":"Reference","previous_headings":"","what":"standardize_record_values — standardize_record_values","title":"standardize_record_values — standardize_record_values","text":"map values dictionary","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/standardize_record_values.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"standardize_record_values — standardize_record_values","text":"","code":"standardize_record_values(x, dictionary = 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+[{"path":[]},{"path":"https://gdrplatform.github.io/gDRimport/PULL_REQUEST_TEMPLATE.html","id":"what-changed","dir":"","previous_headings":"","what":"What changed?","title":"Description","text":"Related JIRA issue:","code":""},{"path":[]},{"path":"https://gdrplatform.github.io/gDRimport/PULL_REQUEST_TEMPLATE.html","id":"checklist-for-sustainable-code-base","dir":"","previous_headings":"","what":"Checklist for sustainable code base","title":"Description","text":"added tests code changed/added added documentation code changed/added made sure naming new functions self-explanatory consistent","code":""},{"path":"https://gdrplatform.github.io/gDRimport/PULL_REQUEST_TEMPLATE.html","id":"logistic-checklist","dir":"","previous_headings":"","what":"Logistic checklist","title":"Description","text":"Package version bumped Changelog updated","code":""},{"path":[]},{"path":"https://gdrplatform.github.io/gDRimport/articles/ConvertingMAEtoPharmacoSet.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"Converting a gDR-generated MultiAssayExperiment object into a PharmacoSet","text":"PharmacoGx package popular tool Bioconductor project within field bioinformatics computational biology. Whereas gDR package valuable tool provides framework import, processing, analysism visualization high-dimensional drug response data, PharmacoGx package provides functionality containerize processed drug response genomic data perform pharmacogenomic analyses. data structure used PharmacoGx described PharamcoSet class, inherited CoreGx::CoreSet. Inspired SummarizedExperiment class, new data structure class called TreatmentResponseExperiment developed store drug response data within PharmacoSet. collaboration BHKLab, developed functionality convert gDR-generated MultiAssayExperiment (MAE) object PharmacoSet object (see ConvertingPharmacoSetToGDR vignette convert PharmacoSet gDR object).","code":""},{"path":"https://gdrplatform.github.io/gDRimport/articles/ConvertingMAEtoPharmacoSet.html","id":"loading-the-gdr-generated-mae-object","dir":"Articles","previous_headings":"","what":"Loading the gDR-generated MAE object","title":"Converting a gDR-generated MultiAssayExperiment object into a PharmacoSet","text":"workflow assumes already generated MAE object using gDR package. load MAE object generated using data KW. Song et al, 2022 study. MAE contains two drugs (treatments) 7 cell lines (samples).","code":"(mae <- qs::qread(     system.file(\"extdata\", \"kyung2022mae\", \"MAE_E2.qs\", package = \"gDRimport\")   ) ) #> A MultiAssayExperiment object of 2 listed #>  experiments with user-defined names and respective classes. #>  Containing an ExperimentList class object of length 2: #>  [1] matrix: SummarizedExperiment with 1 rows and 7 columns #>  [2] single-agent: SummarizedExperiment with 2 rows and 7 columns #> Functionality: #>  experiments() - obtain the ExperimentList instance #>  colData() - the primary/phenotype DataFrame #>  sampleMap() - the sample coordination DataFrame #>  `$`, `[`, `[[` - extract colData columns, subset, or experiment #>  *Format() - convert into a long or wide DataFrame #>  assays() - convert ExperimentList to a SimpleList of matrices #>  exportClass() - save data to flat files"},{"path":"https://gdrplatform.github.io/gDRimport/articles/ConvertingMAEtoPharmacoSet.html","id":"converting-the-mae-object-into-a-pharmacoset-object","dir":"Articles","previous_headings":"","what":"Converting the MAE object into a PharmacoSet object","title":"Converting a gDR-generated MultiAssayExperiment object into a PharmacoSet","text":"First view experiments assays within MultiAssayExperiment object. now convert MAE object PharmacoSet object. need provide name data object, example use name study. can now view PharmacoSet object. can view information drugs cell lines PharmacoSet object using treatment sample slots:","code":"gDRutils::MAEpply(mae, assays) #> $matrix #> List of length 14 #> names(14): RawTreated Controls Normalized ... CIScore_50 CIScore_80 Metrics #>  #> $`single-agent` #> List of length 5 #> names(5): RawTreated Controls Normalized Averaged Metrics pset <- convert_MAE_to_PSet(mae, pset_name=\"Kyung2022\") pset #> <PharmacoSet> #> Name:  Kyung2022  #> Date Created:  Mon Dec  9 10:53:32 2024  #> Number of samples:  7  #> Molecular profiles: #>    A MultiAssayExperiment object of 1 listed #>    experiment with a user-defined name and respective class. #>    Containing an ExperimentList class object of length 1: #>    [1] emptySE: SummarizedExperiment with 0 rows and 7 columns  #> Treatment response: #>    <TreatmentResponseExperiment>  #>   dim:  3 7  #>   assays(14): RawTreated Controls Normalized Averaged SmoothMatrix BlissExcess #>     HSAExcess all_iso_points isobolograms BlissScore HSAScore CIScore_50 #>     CIScore_80 Metrics  #>   rownames(3): G02001876_Palbociclib_CDK4|CDK6_168 G02967907_GDC-0077_PI3K-A_168 G02967907_GDC-0077_PI3K-A_G02001876_Palbociclib_CDK4|CDK6_vehicle_vehicle_168  #>   rowData(10): treatmentid Gnumber DrugName ... DrugName_3 drug_moa_3 Duration  #>   colnames(7): CL129757_MCF-7_Breast_MCF-7_unknown_30 CL130218_BT-474_Breast_BT-474_unknown_70 CL130742_T-47D_Breast_T-47D_unknown_60 ... CL131873_HCC1428_Breast_HCC1428_unknown_74 CL131891_EFM-19_Breast_EFM-19_unknown_64 CL131903_BT-483_Breast_BT-483_unknown_130  #>   colData(7): sampleid clid CellLineName ... parental_identifier subtype ReferenceDivisionTime  #>   metadata(0): none head(treatmentInfo(pset)) #>                                                                     treatmentid #> 1 G02967907_GDC-0077_PI3K-A_G02001876_Palbociclib_CDK4|CDK6_vehicle_vehicle_168 #> 2                                           G02001876_Palbociclib_CDK4|CDK6_168 #> 3                                                 G02967907_GDC-0077_PI3K-A_168 #>     Gnumber    DrugName  drug_moa Gnumber_2  DrugName_2 drug_moa_2 DrugName_3 #> 1 G02967907    GDC-0077    PI3K-A G02001876 Palbociclib  CDK4|CDK6    vehicle #> 2 G02001876 Palbociclib CDK4|CDK6      <NA>        <NA>       <NA>       <NA> #> 3 G02967907    GDC-0077    PI3K-A      <NA>        <NA>       <NA>       <NA> #>   drug_moa_3 Duration #> 1    vehicle      168 #> 2       <NA>      168 #> 3       <NA>      168  head(sampleInfo(pset)) #>                                                                              sampleid #> CL129757_MCF-7_Breast_MCF-7_unknown_30         CL129757_MCF-7_Breast_MCF-7_unknown_30 #> CL130218_BT-474_Breast_BT-474_unknown_70     CL130218_BT-474_Breast_BT-474_unknown_70 #> CL130742_T-47D_Breast_T-47D_unknown_60         CL130742_T-47D_Breast_T-47D_unknown_60 #> CL131438_CAMA-1_Breast_CAMA-1_unknown_53     CL131438_CAMA-1_Breast_CAMA-1_unknown_53 #> CL131873_HCC1428_Breast_HCC1428_unknown_74 CL131873_HCC1428_Breast_HCC1428_unknown_74 #> CL131891_EFM-19_Breast_EFM-19_unknown_64     CL131891_EFM-19_Breast_EFM-19_unknown_64 #>                                                clid CellLineName Tissue #> CL129757_MCF-7_Breast_MCF-7_unknown_30     CL129757        MCF-7 Breast #> CL130218_BT-474_Breast_BT-474_unknown_70   CL130218       BT-474 Breast #> CL130742_T-47D_Breast_T-47D_unknown_60     CL130742        T-47D Breast #> CL131438_CAMA-1_Breast_CAMA-1_unknown_53   CL131438       CAMA-1 Breast #> CL131873_HCC1428_Breast_HCC1428_unknown_74 CL131873      HCC1428 Breast #> CL131891_EFM-19_Breast_EFM-19_unknown_64   CL131891       EFM-19 Breast #>                                            parental_identifier subtype #> CL129757_MCF-7_Breast_MCF-7_unknown_30                   MCF-7 unknown #> CL130218_BT-474_Breast_BT-474_unknown_70                BT-474 unknown #> CL130742_T-47D_Breast_T-47D_unknown_60                   T-47D unknown #> CL131438_CAMA-1_Breast_CAMA-1_unknown_53                CAMA-1 unknown #> CL131873_HCC1428_Breast_HCC1428_unknown_74             HCC1428 unknown #> CL131891_EFM-19_Breast_EFM-19_unknown_64                EFM-19 unknown #>                                            ReferenceDivisionTime batchid #> CL129757_MCF-7_Breast_MCF-7_unknown_30                        30       1 #> CL130218_BT-474_Breast_BT-474_unknown_70                      70       1 #> CL130742_T-47D_Breast_T-47D_unknown_60                        60       1 #> CL131438_CAMA-1_Breast_CAMA-1_unknown_53                      53       1 #> CL131873_HCC1428_Breast_HCC1428_unknown_74                    74       1 #> CL131891_EFM-19_Breast_EFM-19_unknown_64                      64       1"},{"path":"https://gdrplatform.github.io/gDRimport/articles/ConvertingMAEtoPharmacoSet.html","id":"treatmentresponseexperiment-object","dir":"Articles","previous_headings":"","what":"TreatmentResponseExperiment Object","title":"Converting a gDR-generated MultiAssayExperiment object into a PharmacoSet","text":"TreatmentResponseExperiment new class developed store drug response data within PharmacoSet object. vignette cover basics class, however information, please refer PharmacoSet vignette TreatmentResponseExperiment****.","code":""},{"path":"https://gdrplatform.github.io/gDRimport/articles/ConvertingMAEtoPharmacoSet.html","id":"row-and-column-names","dir":"Articles","previous_headings":"TreatmentResponseExperiment Object","what":"Row and Column Names","title":"Converting a gDR-generated MultiAssayExperiment object into a PharmacoSet","text":"","code":"tre <- treatmentResponse(pset) head(rownames(tre)) #> [1] \"G02001876_Palbociclib_CDK4|CDK6_168\"                                           #> [2] \"G02967907_GDC-0077_PI3K-A_168\"                                                 #> [3] \"G02967907_GDC-0077_PI3K-A_G02001876_Palbociclib_CDK4|CDK6_vehicle_vehicle_168\" head(rowData(tre)) #>                                                                      treatmentid #>                                                                           <char> #> 1:                                           G02001876_Palbociclib_CDK4|CDK6_168 #> 2:                                                 G02967907_GDC-0077_PI3K-A_168 #> 3: G02967907_GDC-0077_PI3K-A_G02001876_Palbociclib_CDK4|CDK6_vehicle_vehicle_168 #>      Gnumber    DrugName  drug_moa Gnumber_2  DrugName_2 drug_moa_2 DrugName_3 #>       <char>      <char>    <char>    <char>      <char>     <char>     <char> #> 1: G02001876 Palbociclib CDK4|CDK6      <NA>        <NA>       <NA>       <NA> #> 2: G02967907    GDC-0077    PI3K-A      <NA>        <NA>       <NA>       <NA> #> 3: G02967907    GDC-0077    PI3K-A G02001876 Palbociclib  CDK4|CDK6    vehicle #>    drug_moa_3 Duration #>        <char>    <num> #> 1:       <NA>      168 #> 2:       <NA>      168 #> 3:    vehicle      168 head(colnames(tre)) #> [1] \"CL129757_MCF-7_Breast_MCF-7_unknown_30\"     #> [2] \"CL130218_BT-474_Breast_BT-474_unknown_70\"   #> [3] \"CL130742_T-47D_Breast_T-47D_unknown_60\"     #> [4] \"CL131438_CAMA-1_Breast_CAMA-1_unknown_53\"   #> [5] \"CL131873_HCC1428_Breast_HCC1428_unknown_74\" #> [6] \"CL131891_EFM-19_Breast_EFM-19_unknown_64\" head(colData(tre)) #>                                      sampleid     clid CellLineName Tissue #>                                        <char>   <char>       <char> <char> #> 1:     CL129757_MCF-7_Breast_MCF-7_unknown_30 CL129757        MCF-7 Breast #> 2:   CL130218_BT-474_Breast_BT-474_unknown_70 CL130218       BT-474 Breast #> 3:     CL130742_T-47D_Breast_T-47D_unknown_60 CL130742        T-47D Breast #> 4:   CL131438_CAMA-1_Breast_CAMA-1_unknown_53 CL131438       CAMA-1 Breast #> 5: CL131873_HCC1428_Breast_HCC1428_unknown_74 CL131873      HCC1428 Breast #> 6:   CL131891_EFM-19_Breast_EFM-19_unknown_64 CL131891       EFM-19 Breast #>    parental_identifier subtype ReferenceDivisionTime #>                 <char>  <char>                 <num> #> 1:               MCF-7 unknown                    30 #> 2:              BT-474 unknown                    70 #> 3:               T-47D unknown                    60 #> 4:              CAMA-1 unknown                    53 #> 5:             HCC1428 unknown                    74 #> 6:              EFM-19 unknown                    64"},{"path":"https://gdrplatform.github.io/gDRimport/articles/ConvertingMAEtoPharmacoSet.html","id":"data-table-subsetting","dir":"Articles","previous_headings":"TreatmentResponseExperiment Object","what":"data.table Subsetting","title":"Converting a gDR-generated MultiAssayExperiment object into a PharmacoSet","text":"addition regex queries, TreatmentResponseExperiment object supports arbitrarily complex subset queries using data.table API. access API, need use . function, allows pass raw R expressions evaluated inside j arguments dataTable[, j]. example want subset rows cell line “CL131891_EFM-19_Breast_EFM-19_unknown_64” drug “G02967907_GDC-0077_PI3K-A_168”. can also invert matches subset columns rowData colData:","code":"tre[   .(treatmentid==\"G02967907_GDC-0077_PI3K-A_168\"), # query on row   .(sampleid==\"CL131891_EFM-19_Breast_EFM-19_unknown_64\") # query on column ] #> <TreatmentResponseExperiment>  #> dim:  1 1  #> assays(14): RawTreated Controls Normalized Averaged SmoothMatrix BlissExcess #>   HSAExcess all_iso_points isobolograms BlissScore HSAScore CIScore_50 #>   CIScore_80 Metrics  #> rownames(1): G02967907_GDC-0077_PI3K-A_168  #> rowData(10): treatmentid Gnumber DrugName ... DrugName_3 drug_moa_3 Duration  #> colnames(1): CL131891_EFM-19_Breast_EFM-19_unknown_64  #> colData(7): sampleid clid CellLineName ... parental_identifier subtype ReferenceDivisionTime  #> metadata(0): none tre[   .(treatmentid!=\"G02967907_GDC-0077_PI3K-A_168\"), # query on row   .(sampleid!=\"CL131891_EFM-19_Breast_EFM-19_unknown_64\") # query on column ] #> <TreatmentResponseExperiment>  #> dim:  2 6  #> assays(14): RawTreated Controls Normalized Averaged SmoothMatrix BlissExcess #>   HSAExcess all_iso_points isobolograms BlissScore HSAScore CIScore_50 #>   CIScore_80 Metrics  #> rownames(2): G02001876_Palbociclib_CDK4|CDK6_168 G02967907_GDC-0077_PI3K-A_G02001876_Palbociclib_CDK4|CDK6_vehicle_vehicle_168  #> rowData(10): treatmentid Gnumber DrugName ... DrugName_3 drug_moa_3 Duration  #> colnames(6): CL129757_MCF-7_Breast_MCF-7_unknown_30 CL130218_BT-474_Breast_BT-474_unknown_70 CL130742_T-47D_Breast_T-47D_unknown_60 CL131438_CAMA-1_Breast_CAMA-1_unknown_53 CL131873_HCC1428_Breast_HCC1428_unknown_74 CL131903_BT-483_Breast_BT-483_unknown_130  #> colData(7): sampleid clid CellLineName ... parental_identifier subtype ReferenceDivisionTime  #> metadata(0): none"},{"path":"https://gdrplatform.github.io/gDRimport/articles/ConvertingMAEtoPharmacoSet.html","id":"assays","dir":"Articles","previous_headings":"TreatmentResponseExperiment Object","what":"assays","title":"Converting a gDR-generated MultiAssayExperiment object into a PharmacoSet","text":"assays can viewed assays function. assay column “data_type” references SummarizedExperiment MAE data corresponds .","code":"lapply(assays(tre), head) #> $RawTreated #> Key: <treatmentid, sampleid> #>    treatmentid sampleid drug_moa drug_moa_2 drug_moa_3 DrugName DrugName_2 #>         <char>   <char>   <char>     <char>     <char>   <char>     <char> #> 1:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 2:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 3:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 4:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 5:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 6:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #>    DrugName_3 Duration Gnumber Gnumber_2 CellLineName   clid #>        <char>    <num>  <char>    <char>       <char> <char> #> 1:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 2:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 3:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 4:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 5:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 6:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #>    parental_identifier ReferenceDivisionTime subtype Tissue    data_type #>                 <char>                 <num>  <char> <char>       <char> #> 1:                <NA>                    NA    <NA>   <NA> single-agent #> 2:                <NA>                    NA    <NA>   <NA> single-agent #> 3:                <NA>                    NA    <NA>   <NA> single-agent #> 4:                <NA>                    NA    <NA>   <NA> single-agent #> 5:                <NA>                    NA    <NA>   <NA> single-agent #> 6:                <NA>                    NA    <NA>   <NA> single-agent #>    Concentration Concentration_2   Barcode ReadoutValue BackgroundValue #>            <num>           <num>    <char>        <num>           <num> #> 1:   0.001524158              NA 30190103p       921614             483 #> 2:   0.001524158              NA 30190103p       999312             483 #> 3:   0.001524158              NA 30190103p      1104556             483 #> 4:   0.001524158              NA 30190103p      1122112             483 #> 5:   0.004572471              NA 30190103p       874807             483 #> 6:   0.004572471              NA 30190103p       994797             483 #>                                Template WellRow WellColumn record_id masked #>                                  <char>  <char>     <char>     <int> <lgcl> #> 1: Template_0077_Palbo_7daytreated.xlsx       D         20      2832  FALSE #> 2: Template_0077_Palbo_7daytreated.xlsx       C         20      2831  FALSE #> 3: Template_0077_Palbo_7daytreated.xlsx       D         19      2830  FALSE #> 4: Template_0077_Palbo_7daytreated.xlsx       C         19      2829  FALSE #> 5: Template_0077_Palbo_7daytreated.xlsx       C         18      2835  FALSE #> 6: Template_0077_Palbo_7daytreated.xlsx       D         18      2836  FALSE #>    CorrectedReadout swap_sa i.Gnumber  i.DrugName i.drug_moa i.Gnumber_2 #>               <num>  <lgcl>    <char>      <char>     <char>      <char> #> 1:           921131      NA G02001876 Palbociclib  CDK4|CDK6        <NA> #> 2:           998829      NA G02001876 Palbociclib  CDK4|CDK6        <NA> #> 3:          1104073      NA G02001876 Palbociclib  CDK4|CDK6        <NA> #> 4:          1121629      NA G02001876 Palbociclib  CDK4|CDK6        <NA> #> 5:           874324      NA G02001876 Palbociclib  CDK4|CDK6        <NA> #> 6:           994314      NA G02001876 Palbociclib  CDK4|CDK6        <NA> #>    i.DrugName_2 i.drug_moa_2 i.DrugName_3 i.drug_moa_3 i.Duration   i.clid #>          <char>       <char>       <char>       <char>      <num>   <char> #> 1:         <NA>         <NA>         <NA>         <NA>        168 CL129757 #> 2:         <NA>         <NA>         <NA>         <NA>        168 CL129757 #> 3:         <NA>         <NA>         <NA>         <NA>        168 CL129757 #> 4:         <NA>         <NA>         <NA>         <NA>        168 CL129757 #> 5:         <NA>         <NA>         <NA>         <NA>        168 CL129757 #> 6:         <NA>         <NA>         <NA>         <NA>        168 CL129757 #>    i.CellLineName i.Tissue i.parental_identifier i.subtype #>            <char>   <char>                <char>    <char> #> 1:          MCF-7   Breast                 MCF-7   unknown #> 2:          MCF-7   Breast                 MCF-7   unknown #> 3:          MCF-7   Breast                 MCF-7   unknown #> 4:          MCF-7   Breast                 MCF-7   unknown #> 5:          MCF-7   Breast                 MCF-7   unknown #> 6:          MCF-7   Breast                 MCF-7   unknown #>    i.ReferenceDivisionTime #>                      <num> #> 1:                      30 #> 2:                      30 #> 3:                      30 #> 4:                      30 #> 5:                      30 #> 6:                      30 #>  #> $Controls #> Key: <treatmentid, sampleid> #>    treatmentid sampleid drug_moa drug_moa_2 drug_moa_3 DrugName DrugName_2 #>         <char>   <char>   <char>     <char>     <char>   <char>     <char> #> 1:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 2:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 3:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 4:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 5:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 6:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #>    DrugName_3 Duration Gnumber Gnumber_2 CellLineName   clid #>        <char>    <num>  <char>    <char>       <char> <char> #> 1:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 2:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 3:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 4:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 5:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 6:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #>    parental_identifier ReferenceDivisionTime subtype Tissue    data_type #>                 <char>                 <num>  <char> <char>       <char> #> 1:                <NA>                    NA    <NA>   <NA> single-agent #> 2:                <NA>                    NA    <NA>   <NA> single-agent #> 3:                <NA>                    NA    <NA>   <NA> single-agent #> 4:                <NA>                    NA    <NA>   <NA> single-agent #> 5:                <NA>                    NA    <NA>   <NA> single-agent #> 6:                <NA>                    NA    <NA>   <NA> single-agent #>    control_type CorrectedReadout record_id   Barcode isDay0 i.Gnumber #>          <char>            <num>     <int>    <char> <lgcl>    <char> #> 1:  Day0Readout            97219      2401 20190103p   TRUE G02001876 #> 2:  Day0Readout            97219      2402 20190103p   TRUE G02001876 #> 3:  Day0Readout            97219      2403 20190103p   TRUE G02001876 #> 4:  Day0Readout            97219      2404 20190103p   TRUE G02001876 #> 5:  Day0Readout            97219      2405 20190103p   TRUE G02001876 #> 6:  Day0Readout            97219      2406 20190103p   TRUE G02001876 #>     i.DrugName i.drug_moa i.Gnumber_2 i.DrugName_2 i.drug_moa_2 i.DrugName_3 #>         <char>     <char>      <char>       <char>       <char>       <char> #> 1: Palbociclib  CDK4|CDK6        <NA>         <NA>         <NA>         <NA> #> 2: Palbociclib  CDK4|CDK6        <NA>         <NA>         <NA>         <NA> #> 3: Palbociclib  CDK4|CDK6        <NA>         <NA>         <NA>         <NA> #> 4: Palbociclib  CDK4|CDK6        <NA>         <NA>         <NA>         <NA> #> 5: Palbociclib  CDK4|CDK6        <NA>         <NA>         <NA>         <NA> #> 6: Palbociclib  CDK4|CDK6        <NA>         <NA>         <NA>         <NA> #>    i.drug_moa_3 i.Duration   i.clid i.CellLineName i.Tissue #>          <char>      <num>   <char>         <char>   <char> #> 1:         <NA>        168 CL129757          MCF-7   Breast #> 2:         <NA>        168 CL129757          MCF-7   Breast #> 3:         <NA>        168 CL129757          MCF-7   Breast #> 4:         <NA>        168 CL129757          MCF-7   Breast #> 5:         <NA>        168 CL129757          MCF-7   Breast #> 6:         <NA>        168 CL129757          MCF-7   Breast #>    i.parental_identifier i.subtype i.ReferenceDivisionTime #>                   <char>    <char>                   <num> #> 1:                 MCF-7   unknown                      30 #> 2:                 MCF-7   unknown                      30 #> 3:                 MCF-7   unknown                      30 #> 4:                 MCF-7   unknown                      30 #> 5:                 MCF-7   unknown                      30 #> 6:                 MCF-7   unknown                      30 #>  #> $Normalized #> Key: <treatmentid, sampleid> #>    treatmentid sampleid drug_moa drug_moa_2 drug_moa_3 DrugName DrugName_2 #>         <char>   <char>   <char>     <char>     <char>   <char>     <char> #> 1:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 2:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 3:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 4:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 5:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 6:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #>    DrugName_3 Duration Gnumber Gnumber_2 CellLineName   clid #>        <char>    <num>  <char>    <char>       <char> <char> #> 1:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 2:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 3:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 4:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 5:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 6:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #>    parental_identifier ReferenceDivisionTime subtype Tissue    data_type #>                 <char>                 <num>  <char> <char>       <char> #> 1:                <NA>                    NA    <NA>   <NA> single-agent #> 2:                <NA>                    NA    <NA>   <NA> single-agent #> 3:                <NA>                    NA    <NA>   <NA> single-agent #> 4:                <NA>                    NA    <NA>   <NA> single-agent #> 5:                <NA>                    NA    <NA>   <NA> single-agent #> 6:                <NA>                    NA    <NA>   <NA> single-agent #>    Concentration Concentration_2 masked normalization_type      x i.Gnumber #>            <num>           <num> <lgcl>             <fctr>  <num>    <char> #> 1:   0.001524158              NA  FALSE                 RV 0.8253 G02001876 #> 2:   0.001524158              NA  FALSE                 RV 0.8949 G02001876 #> 3:   0.001524158              NA  FALSE                 RV 0.9892 G02001876 #> 4:   0.001524158              NA  FALSE                 RV 1.0049 G02001876 #> 5:   0.004572471              NA  FALSE                 RV 0.7833 G02001876 #> 6:   0.004572471              NA  FALSE                 RV 0.8908 G02001876 #>     i.DrugName i.drug_moa i.Gnumber_2 i.DrugName_2 i.drug_moa_2 i.DrugName_3 #>         <char>     <char>      <char>       <char>       <char>       <char> #> 1: Palbociclib  CDK4|CDK6        <NA>         <NA>         <NA>         <NA> #> 2: Palbociclib  CDK4|CDK6        <NA>         <NA>         <NA>         <NA> #> 3: Palbociclib  CDK4|CDK6        <NA>         <NA>         <NA>         <NA> #> 4: Palbociclib  CDK4|CDK6        <NA>         <NA>         <NA>         <NA> #> 5: Palbociclib  CDK4|CDK6        <NA>         <NA>         <NA>         <NA> #> 6: Palbociclib  CDK4|CDK6        <NA>         <NA>         <NA>         <NA> #>    i.drug_moa_3 i.Duration   i.clid i.CellLineName i.Tissue #>          <char>      <num>   <char>         <char>   <char> #> 1:         <NA>        168 CL129757          MCF-7   Breast #> 2:         <NA>        168 CL129757          MCF-7   Breast #> 3:         <NA>        168 CL129757          MCF-7   Breast #> 4:         <NA>        168 CL129757          MCF-7   Breast #> 5:         <NA>        168 CL129757          MCF-7   Breast #> 6:         <NA>        168 CL129757          MCF-7   Breast #>    i.parental_identifier i.subtype i.ReferenceDivisionTime #>                   <char>    <char>                   <num> #> 1:                 MCF-7   unknown                      30 #> 2:                 MCF-7   unknown                      30 #> 3:                 MCF-7   unknown                      30 #> 4:                 MCF-7   unknown                      30 #> 5:                 MCF-7   unknown                      30 #> 6:                 MCF-7   unknown                      30 #>  #> $Averaged #> Key: <treatmentid, sampleid> #>    treatmentid sampleid drug_moa drug_moa_2 drug_moa_3 DrugName DrugName_2 #>         <char>   <char>   <char>     <char>     <char>   <char>     <char> #> 1:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 2:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 3:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 4:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 5:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 6:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #>    DrugName_3 Duration Gnumber Gnumber_2 CellLineName   clid #>        <char>    <num>  <char>    <char>       <char> <char> #> 1:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 2:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 3:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 4:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 5:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 6:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #>    parental_identifier ReferenceDivisionTime subtype Tissue    data_type #>                 <char>                 <num>  <char> <char>       <char> #> 1:                <NA>                    NA    <NA>   <NA> single-agent #> 2:                <NA>                    NA    <NA>   <NA> single-agent #> 3:                <NA>                    NA    <NA>   <NA> single-agent #> 4:                <NA>                    NA    <NA>   <NA> single-agent #> 5:                <NA>                    NA    <NA>   <NA> single-agent #> 6:                <NA>                    NA    <NA>   <NA> single-agent #>    normalization_type Concentration Concentration_2        x      x_std #>                <fctr>         <num>           <num>    <num>      <num> #> 1:                 RV   0.001524158              NA 0.928575 0.08426274 #> 2:                 GR   0.001524158              NA 0.952225 0.05675581 #> 3:                 RV   0.004572471              NA 0.885050 0.07091133 #> 4:                 GR   0.004572471              NA 0.923000 0.04998000 #> 5:                 RV   0.013717406              NA 0.843800 0.05585201 #> 6:                 GR   0.013717406              NA 0.894475 0.04037973 #>    i.Gnumber  i.DrugName i.drug_moa i.Gnumber_2 i.DrugName_2 i.drug_moa_2 #>       <char>      <char>     <char>      <char>       <char>       <char> #> 1: G02001876 Palbociclib  CDK4|CDK6        <NA>         <NA>         <NA> #> 2: G02001876 Palbociclib  CDK4|CDK6        <NA>         <NA>         <NA> #> 3: G02001876 Palbociclib  CDK4|CDK6        <NA>         <NA>         <NA> #> 4: G02001876 Palbociclib  CDK4|CDK6        <NA>         <NA>         <NA> #> 5: G02001876 Palbociclib  CDK4|CDK6        <NA>         <NA>         <NA> #> 6: G02001876 Palbociclib  CDK4|CDK6        <NA>         <NA>         <NA> #>    i.DrugName_3 i.drug_moa_3 i.Duration   i.clid i.CellLineName i.Tissue #>          <char>       <char>      <num>   <char>         <char>   <char> #> 1:         <NA>         <NA>        168 CL129757          MCF-7   Breast #> 2:         <NA>         <NA>        168 CL129757          MCF-7   Breast #> 3:         <NA>         <NA>        168 CL129757          MCF-7   Breast #> 4:         <NA>         <NA>        168 CL129757          MCF-7   Breast #> 5:         <NA>         <NA>        168 CL129757          MCF-7   Breast #> 6:         <NA>         <NA>        168 CL129757          MCF-7   Breast #>    i.parental_identifier i.subtype i.ReferenceDivisionTime #>                   <char>    <char>                   <num> #> 1:                 MCF-7   unknown                      30 #> 2:                 MCF-7   unknown                      30 #> 3:                 MCF-7   unknown                      30 #> 4:                 MCF-7   unknown                      30 #> 5:                 MCF-7   unknown                      30 #> 6:                 MCF-7   unknown                      30 #>  #> $SmoothMatrix #> Key: <treatmentid, sampleid> #>    treatmentid sampleid drug_moa drug_moa_2 drug_moa_3 DrugName DrugName_2 #>         <char>   <char>   <char>     <char>     <char>   <char>     <char> #> 1:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 2:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 3:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 4:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 5:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 6:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #>    DrugName_3 Duration Gnumber Gnumber_2 CellLineName   clid #>        <char>    <num>  <char>    <char>       <char> <char> #> 1:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 2:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 3:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 4:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 5:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 6:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #>    parental_identifier ReferenceDivisionTime subtype Tissue    data_type #>                 <char>                 <num>  <char> <char>       <char> #> 1:                <NA>                    NA    <NA>   <NA> single-agent #> 2:                <NA>                    NA    <NA>   <NA> single-agent #> 3:                <NA>                    NA    <NA>   <NA> single-agent #> 4:                <NA>                    NA    <NA>   <NA> single-agent #> 5:                <NA>                    NA    <NA>   <NA> single-agent #> 6:                <NA>                    NA    <NA>   <NA> single-agent #>    Concentration Concentration_2     x normalization_type i.Gnumber  i.DrugName #>            <num>           <num> <num>             <char>    <char>      <char> #> 1:            NA              NA    NA               <NA> G02001876 Palbociclib #> 2:            NA              NA    NA               <NA> G02001876 Palbociclib #> 3:            NA              NA    NA               <NA> G02001876 Palbociclib #> 4:            NA              NA    NA               <NA> G02001876 Palbociclib #> 5:            NA              NA    NA               <NA> G02967907    GDC-0077 #> 6:            NA              NA    NA               <NA> G02967907    GDC-0077 #>    i.drug_moa i.Gnumber_2 i.DrugName_2 i.drug_moa_2 i.DrugName_3 i.drug_moa_3 #>        <char>      <char>       <char>       <char>       <char>       <char> #> 1:  CDK4|CDK6        <NA>         <NA>         <NA>         <NA>         <NA> #> 2:  CDK4|CDK6        <NA>         <NA>         <NA>         <NA>         <NA> #> 3:  CDK4|CDK6        <NA>         <NA>         <NA>         <NA>         <NA> #> 4:  CDK4|CDK6        <NA>         <NA>         <NA>         <NA>         <NA> #> 5:     PI3K-A        <NA>         <NA>         <NA>         <NA>         <NA> #> 6:     PI3K-A        <NA>         <NA>         <NA>         <NA>         <NA> #>    i.Duration   i.clid i.CellLineName i.Tissue i.parental_identifier i.subtype #>         <num>   <char>         <char>   <char>                <char>    <char> #> 1:        168 CL129757          MCF-7   Breast                 MCF-7   unknown #> 2:        168 CL130742          T-47D   Breast                 T-47D   unknown #> 3:        168 CL131873        HCC1428   Breast               HCC1428   unknown #> 4:        168 CL131903         BT-483   Breast                BT-483   unknown #> 5:        168 CL130218         BT-474   Breast                BT-474   unknown #> 6:        168 CL131438         CAMA-1   Breast                CAMA-1   unknown #>    i.ReferenceDivisionTime #>                      <num> #> 1:                      30 #> 2:                      60 #> 3:                      74 #> 4:                     130 #> 5:                      70 #> 6:                      53 #>  #> $BlissExcess #> Key: <treatmentid, sampleid> #>    treatmentid sampleid drug_moa drug_moa_2 drug_moa_3 DrugName DrugName_2 #>         <char>   <char>   <char>     <char>     <char>   <char>     <char> #> 1:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 2:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 3:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 4:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 5:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 6:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #>    DrugName_3 Duration Gnumber Gnumber_2 CellLineName   clid #>        <char>    <num>  <char>    <char>       <char> <char> #> 1:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 2:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 3:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 4:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 5:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 6:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #>    parental_identifier ReferenceDivisionTime subtype Tissue    data_type #>                 <char>                 <num>  <char> <char>       <char> #> 1:                <NA>                    NA    <NA>   <NA> single-agent #> 2:                <NA>                    NA    <NA>   <NA> single-agent #> 3:                <NA>                    NA    <NA>   <NA> single-agent #> 4:                <NA>                    NA    <NA>   <NA> single-agent #> 5:                <NA>                    NA    <NA>   <NA> single-agent #> 6:                <NA>                    NA    <NA>   <NA> single-agent #>    Concentration Concentration_2     x normalization_type i.Gnumber  i.DrugName #>            <num>           <num> <num>             <char>    <char>      <char> #> 1:            NA              NA    NA               <NA> G02001876 Palbociclib #> 2:            NA              NA    NA               <NA> G02001876 Palbociclib #> 3:            NA              NA    NA               <NA> G02001876 Palbociclib #> 4:            NA              NA    NA               <NA> G02001876 Palbociclib #> 5:            NA              NA    NA               <NA> G02967907    GDC-0077 #> 6:            NA              NA    NA               <NA> G02967907    GDC-0077 #>    i.drug_moa i.Gnumber_2 i.DrugName_2 i.drug_moa_2 i.DrugName_3 i.drug_moa_3 #>        <char>      <char>       <char>       <char>       <char>       <char> #> 1:  CDK4|CDK6        <NA>         <NA>         <NA>         <NA>         <NA> #> 2:  CDK4|CDK6        <NA>         <NA>         <NA>         <NA>         <NA> #> 3:  CDK4|CDK6        <NA>         <NA>         <NA>         <NA>         <NA> #> 4:  CDK4|CDK6        <NA>         <NA>         <NA>         <NA>         <NA> #> 5:     PI3K-A        <NA>         <NA>         <NA>         <NA>         <NA> #> 6:     PI3K-A        <NA>         <NA>         <NA>         <NA>         <NA> #>    i.Duration   i.clid i.CellLineName i.Tissue i.parental_identifier i.subtype #>         <num>   <char>         <char>   <char>                <char>    <char> #> 1:        168 CL129757          MCF-7   Breast                 MCF-7   unknown #> 2:        168 CL130742          T-47D   Breast                 T-47D   unknown #> 3:        168 CL131873        HCC1428   Breast               HCC1428   unknown #> 4:        168 CL131903         BT-483   Breast                BT-483   unknown #> 5:        168 CL130218         BT-474   Breast                BT-474   unknown #> 6:        168 CL131438         CAMA-1   Breast                CAMA-1   unknown #>    i.ReferenceDivisionTime #>                      <num> #> 1:                      30 #> 2:                      60 #> 3:                      74 #> 4:                     130 #> 5:                      70 #> 6:                      53 #>  #> $HSAExcess #> Key: <treatmentid, sampleid> #>    treatmentid sampleid drug_moa drug_moa_2 drug_moa_3 DrugName DrugName_2 #>         <char>   <char>   <char>     <char>     <char>   <char>     <char> #> 1:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 2:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 3:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 4:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 5:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 6:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #>    DrugName_3 Duration Gnumber Gnumber_2 CellLineName   clid #>        <char>    <num>  <char>    <char>       <char> <char> #> 1:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 2:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 3:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 4:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 5:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 6:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #>    parental_identifier ReferenceDivisionTime subtype Tissue    data_type #>                 <char>                 <num>  <char> <char>       <char> #> 1:                <NA>                    NA    <NA>   <NA> single-agent #> 2:                <NA>                    NA    <NA>   <NA> single-agent #> 3:                <NA>                    NA    <NA>   <NA> single-agent #> 4:                <NA>                    NA    <NA>   <NA> single-agent #> 5:                <NA>                    NA    <NA>   <NA> single-agent #> 6:                <NA>                    NA    <NA>   <NA> single-agent #>    Concentration Concentration_2     x normalization_type i.Gnumber  i.DrugName #>            <num>           <num> <num>             <char>    <char>      <char> #> 1:            NA              NA    NA               <NA> G02001876 Palbociclib #> 2:            NA              NA    NA               <NA> G02001876 Palbociclib #> 3:            NA              NA    NA               <NA> G02001876 Palbociclib #> 4:            NA              NA    NA               <NA> G02001876 Palbociclib #> 5:            NA              NA    NA               <NA> G02967907    GDC-0077 #> 6:            NA              NA    NA               <NA> G02967907    GDC-0077 #>    i.drug_moa i.Gnumber_2 i.DrugName_2 i.drug_moa_2 i.DrugName_3 i.drug_moa_3 #>        <char>      <char>       <char>       <char>       <char>       <char> #> 1:  CDK4|CDK6        <NA>         <NA>         <NA>         <NA>         <NA> #> 2:  CDK4|CDK6        <NA>         <NA>         <NA>         <NA>         <NA> #> 3:  CDK4|CDK6        <NA>         <NA>         <NA>         <NA>         <NA> #> 4:  CDK4|CDK6        <NA>         <NA>         <NA>         <NA>         <NA> #> 5:     PI3K-A        <NA>         <NA>         <NA>         <NA>         <NA> #> 6:     PI3K-A        <NA>         <NA>         <NA>         <NA>         <NA> #>    i.Duration   i.clid i.CellLineName i.Tissue i.parental_identifier i.subtype #>         <num>   <char>         <char>   <char>                <char>    <char> #> 1:        168 CL129757          MCF-7   Breast                 MCF-7   unknown #> 2:        168 CL130742          T-47D   Breast                 T-47D   unknown #> 3:        168 CL131873        HCC1428   Breast               HCC1428   unknown #> 4:        168 CL131903         BT-483   Breast                BT-483   unknown #> 5:        168 CL130218         BT-474   Breast                BT-474   unknown #> 6:        168 CL131438         CAMA-1   Breast                CAMA-1   unknown #>    i.ReferenceDivisionTime #>                      <num> #> 1:                      30 #> 2:                      60 #> 3:                      74 #> 4:                     130 #> 5:                      70 #> 6:                      53 #>  #> $all_iso_points #> Key: <treatmentid, sampleid> #>    treatmentid sampleid drug_moa drug_moa_2 drug_moa_3 DrugName DrugName_2 #>         <char>   <char>   <char>     <char>     <char>   <char>     <char> #> 1:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 2:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 3:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 4:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 5:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 6:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #>    DrugName_3 Duration Gnumber Gnumber_2 CellLineName   clid #>        <char>    <num>  <char>    <char>       <char> <char> #> 1:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 2:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 3:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 4:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 5:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 6:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #>    parental_identifier ReferenceDivisionTime subtype Tissue    data_type #>                 <char>                 <num>  <char> <char>       <char> #> 1:                <NA>                    NA    <NA>   <NA> single-agent #> 2:                <NA>                    NA    <NA>   <NA> single-agent #> 3:                <NA>                    NA    <NA>   <NA> single-agent #> 4:                <NA>                    NA    <NA>   <NA> single-agent #> 5:                <NA>                    NA    <NA>   <NA> single-agent #> 6:                <NA>                    NA    <NA>   <NA> single-agent #>    normalization_type i.Gnumber  i.DrugName i.drug_moa i.Gnumber_2 i.DrugName_2 #>                <char>    <char>      <char>     <char>      <char>       <char> #> 1:               <NA> G02001876 Palbociclib  CDK4|CDK6        <NA>         <NA> #> 2:               <NA> G02001876 Palbociclib  CDK4|CDK6        <NA>         <NA> #> 3:               <NA> G02001876 Palbociclib  CDK4|CDK6        <NA>         <NA> #> 4:               <NA> G02001876 Palbociclib  CDK4|CDK6        <NA>         <NA> #> 5:               <NA> G02967907    GDC-0077     PI3K-A        <NA>         <NA> #> 6:               <NA> G02967907    GDC-0077     PI3K-A        <NA>         <NA> #>    i.drug_moa_2 i.DrugName_3 i.drug_moa_3 i.Duration   i.clid i.CellLineName #>          <char>       <char>       <char>      <num>   <char>         <char> #> 1:         <NA>         <NA>         <NA>        168 CL129757          MCF-7 #> 2:         <NA>         <NA>         <NA>        168 CL130742          T-47D #> 3:         <NA>         <NA>         <NA>        168 CL131873        HCC1428 #> 4:         <NA>         <NA>         <NA>        168 CL131903         BT-483 #> 5:         <NA>         <NA>         <NA>        168 CL130218         BT-474 #> 6:         <NA>         <NA>         <NA>        168 CL131438         CAMA-1 #>    i.Tissue i.parental_identifier i.subtype i.ReferenceDivisionTime      x #>      <char>                <char>    <char>                   <num> <lgcl> #> 1:   Breast                 MCF-7   unknown                      30     NA #> 2:   Breast                 T-47D   unknown                      60     NA #> 3:   Breast               HCC1428   unknown                      74     NA #> 4:   Breast                BT-483   unknown                     130     NA #> 5:   Breast                BT-474   unknown                      70     NA #> 6:   Breast                CAMA-1   unknown                      53     NA #>  #> $isobolograms #> Key: <treatmentid, sampleid> #>    treatmentid sampleid drug_moa drug_moa_2 drug_moa_3 DrugName DrugName_2 #>         <char>   <char>   <char>     <char>     <char>   <char>     <char> #> 1:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 2:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 3:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 4:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 5:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 6:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #>    DrugName_3 Duration Gnumber Gnumber_2 CellLineName   clid #>        <char>    <num>  <char>    <char>       <char> <char> #> 1:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 2:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 3:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 4:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 5:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 6:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #>    parental_identifier ReferenceDivisionTime subtype Tissue    data_type #>                 <char>                 <num>  <char> <char>       <char> #> 1:                <NA>                    NA    <NA>   <NA> single-agent #> 2:                <NA>                    NA    <NA>   <NA> single-agent #> 3:                <NA>                    NA    <NA>   <NA> single-agent #> 4:                <NA>                    NA    <NA>   <NA> single-agent #> 5:                <NA>                    NA    <NA>   <NA> single-agent #> 6:                <NA>                    NA    <NA>   <NA> single-agent #>    normalization_type i.Gnumber  i.DrugName i.drug_moa i.Gnumber_2 i.DrugName_2 #>                <char>    <char>      <char>     <char>      <char>       <char> #> 1:               <NA> G02001876 Palbociclib  CDK4|CDK6        <NA>         <NA> #> 2:               <NA> G02001876 Palbociclib  CDK4|CDK6        <NA>         <NA> #> 3:               <NA> G02001876 Palbociclib  CDK4|CDK6        <NA>         <NA> #> 4:               <NA> G02001876 Palbociclib  CDK4|CDK6        <NA>         <NA> #> 5:               <NA> G02967907    GDC-0077     PI3K-A        <NA>         <NA> #> 6:               <NA> G02967907    GDC-0077     PI3K-A        <NA>         <NA> #>    i.drug_moa_2 i.DrugName_3 i.drug_moa_3 i.Duration   i.clid i.CellLineName #>          <char>       <char>       <char>      <num>   <char>         <char> #> 1:         <NA>         <NA>         <NA>        168 CL129757          MCF-7 #> 2:         <NA>         <NA>         <NA>        168 CL130742          T-47D #> 3:         <NA>         <NA>         <NA>        168 CL131873        HCC1428 #> 4:         <NA>         <NA>         <NA>        168 CL131903         BT-483 #> 5:         <NA>         <NA>         <NA>        168 CL130218         BT-474 #> 6:         <NA>         <NA>         <NA>        168 CL131438         CAMA-1 #>    i.Tissue i.parental_identifier i.subtype i.ReferenceDivisionTime      x #>      <char>                <char>    <char>                   <num> <lgcl> #> 1:   Breast                 MCF-7   unknown                      30     NA #> 2:   Breast                 T-47D   unknown                      60     NA #> 3:   Breast               HCC1428   unknown                      74     NA #> 4:   Breast                BT-483   unknown                     130     NA #> 5:   Breast                BT-474   unknown                      70     NA #> 6:   Breast                CAMA-1   unknown                      53     NA #>  #> $BlissScore #> Key: <treatmentid, sampleid> #>    treatmentid sampleid drug_moa drug_moa_2 drug_moa_3 DrugName DrugName_2 #>         <char>   <char>   <char>     <char>     <char>   <char>     <char> #> 1:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 2:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 3:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 4:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 5:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 6:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #>    DrugName_3 Duration Gnumber Gnumber_2 CellLineName   clid #>        <char>    <num>  <char>    <char>       <char> <char> #> 1:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 2:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 3:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 4:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 5:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 6:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #>    parental_identifier ReferenceDivisionTime subtype Tissue    data_type #>                 <char>                 <num>  <char> <char>       <char> #> 1:                <NA>                    NA    <NA>   <NA> single-agent #> 2:                <NA>                    NA    <NA>   <NA> single-agent #> 3:                <NA>                    NA    <NA>   <NA> single-agent #> 4:                <NA>                    NA    <NA>   <NA> single-agent #> 5:                <NA>                    NA    <NA>   <NA> single-agent #> 6:                <NA>                    NA    <NA>   <NA> single-agent #>    normalization_type     x i.Gnumber  i.DrugName i.drug_moa i.Gnumber_2 #>                <char> <num>    <char>      <char>     <char>      <char> #> 1:               <NA>    NA G02001876 Palbociclib  CDK4|CDK6        <NA> #> 2:               <NA>    NA G02001876 Palbociclib  CDK4|CDK6        <NA> #> 3:               <NA>    NA G02001876 Palbociclib  CDK4|CDK6        <NA> #> 4:               <NA>    NA G02001876 Palbociclib  CDK4|CDK6        <NA> #> 5:               <NA>    NA G02967907    GDC-0077     PI3K-A        <NA> #> 6:               <NA>    NA G02967907    GDC-0077     PI3K-A        <NA> #>    i.DrugName_2 i.drug_moa_2 i.DrugName_3 i.drug_moa_3 i.Duration   i.clid #>          <char>       <char>       <char>       <char>      <num>   <char> #> 1:         <NA>         <NA>         <NA>         <NA>        168 CL129757 #> 2:         <NA>         <NA>         <NA>         <NA>        168 CL130742 #> 3:         <NA>         <NA>         <NA>         <NA>        168 CL131873 #> 4:         <NA>         <NA>         <NA>         <NA>        168 CL131903 #> 5:         <NA>         <NA>         <NA>         <NA>        168 CL130218 #> 6:         <NA>         <NA>         <NA>         <NA>        168 CL131438 #>    i.CellLineName i.Tissue i.parental_identifier i.subtype #>            <char>   <char>                <char>    <char> #> 1:          MCF-7   Breast                 MCF-7   unknown #> 2:          T-47D   Breast                 T-47D   unknown #> 3:        HCC1428   Breast               HCC1428   unknown #> 4:         BT-483   Breast                BT-483   unknown #> 5:         BT-474   Breast                BT-474   unknown #> 6:         CAMA-1   Breast                CAMA-1   unknown #>    i.ReferenceDivisionTime #>                      <num> #> 1:                      30 #> 2:                      60 #> 3:                      74 #> 4:                     130 #> 5:                      70 #> 6:                      53 #>  #> $HSAScore #> Key: <treatmentid, sampleid> #>    treatmentid sampleid drug_moa drug_moa_2 drug_moa_3 DrugName DrugName_2 #>         <char>   <char>   <char>     <char>     <char>   <char>     <char> #> 1:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 2:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 3:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 4:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 5:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 6:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #>    DrugName_3 Duration Gnumber Gnumber_2 CellLineName   clid #>        <char>    <num>  <char>    <char>       <char> <char> #> 1:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 2:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 3:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 4:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 5:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 6:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #>    parental_identifier ReferenceDivisionTime subtype Tissue    data_type #>                 <char>                 <num>  <char> <char>       <char> #> 1:                <NA>                    NA    <NA>   <NA> single-agent #> 2:                <NA>                    NA    <NA>   <NA> single-agent #> 3:                <NA>                    NA    <NA>   <NA> single-agent #> 4:                <NA>                    NA    <NA>   <NA> single-agent #> 5:                <NA>                    NA    <NA>   <NA> single-agent #> 6:                <NA>                    NA    <NA>   <NA> single-agent #>    normalization_type     x i.Gnumber  i.DrugName i.drug_moa i.Gnumber_2 #>                <char> <num>    <char>      <char>     <char>      <char> #> 1:               <NA>    NA G02001876 Palbociclib  CDK4|CDK6        <NA> #> 2:               <NA>    NA G02001876 Palbociclib  CDK4|CDK6        <NA> #> 3:               <NA>    NA G02001876 Palbociclib  CDK4|CDK6        <NA> #> 4:               <NA>    NA G02001876 Palbociclib  CDK4|CDK6        <NA> #> 5:               <NA>    NA G02967907    GDC-0077     PI3K-A        <NA> #> 6:               <NA>    NA G02967907    GDC-0077     PI3K-A        <NA> #>    i.DrugName_2 i.drug_moa_2 i.DrugName_3 i.drug_moa_3 i.Duration   i.clid #>          <char>       <char>       <char>       <char>      <num>   <char> #> 1:         <NA>         <NA>         <NA>         <NA>        168 CL129757 #> 2:         <NA>         <NA>         <NA>         <NA>        168 CL130742 #> 3:         <NA>         <NA>         <NA>         <NA>        168 CL131873 #> 4:         <NA>         <NA>         <NA>         <NA>        168 CL131903 #> 5:         <NA>         <NA>         <NA>         <NA>        168 CL130218 #> 6:         <NA>         <NA>         <NA>         <NA>        168 CL131438 #>    i.CellLineName i.Tissue i.parental_identifier i.subtype #>            <char>   <char>                <char>    <char> #> 1:          MCF-7   Breast                 MCF-7   unknown #> 2:          T-47D   Breast                 T-47D   unknown #> 3:        HCC1428   Breast               HCC1428   unknown #> 4:         BT-483   Breast                BT-483   unknown #> 5:         BT-474   Breast                BT-474   unknown #> 6:         CAMA-1   Breast                CAMA-1   unknown #>    i.ReferenceDivisionTime #>                      <num> #> 1:                      30 #> 2:                      60 #> 3:                      74 #> 4:                     130 #> 5:                      70 #> 6:                      53 #>  #> $CIScore_50 #> Key: <treatmentid, sampleid> #>    treatmentid sampleid drug_moa drug_moa_2 drug_moa_3 DrugName DrugName_2 #>         <char>   <char>   <char>     <char>     <char>   <char>     <char> #> 1:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 2:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 3:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 4:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 5:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 6:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #>    DrugName_3 Duration Gnumber Gnumber_2 CellLineName   clid #>        <char>    <num>  <char>    <char>       <char> <char> #> 1:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 2:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 3:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 4:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 5:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 6:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #>    parental_identifier ReferenceDivisionTime subtype Tissue    data_type #>                 <char>                 <num>  <char> <char>       <char> #> 1:                <NA>                    NA    <NA>   <NA> single-agent #> 2:                <NA>                    NA    <NA>   <NA> single-agent #> 3:                <NA>                    NA    <NA>   <NA> single-agent #> 4:                <NA>                    NA    <NA>   <NA> single-agent #> 5:                <NA>                    NA    <NA>   <NA> single-agent #> 6:                <NA>                    NA    <NA>   <NA> single-agent #>    normalization_type      x i.Gnumber  i.DrugName i.drug_moa i.Gnumber_2 #>                <char> <lgcl>    <char>      <char>     <char>      <char> #> 1:               <NA>     NA G02001876 Palbociclib  CDK4|CDK6        <NA> #> 2:               <NA>     NA G02001876 Palbociclib  CDK4|CDK6        <NA> #> 3:               <NA>     NA G02001876 Palbociclib  CDK4|CDK6        <NA> #> 4:               <NA>     NA G02001876 Palbociclib  CDK4|CDK6        <NA> #> 5:               <NA>     NA G02967907    GDC-0077     PI3K-A        <NA> #> 6:               <NA>     NA G02967907    GDC-0077     PI3K-A        <NA> #>    i.DrugName_2 i.drug_moa_2 i.DrugName_3 i.drug_moa_3 i.Duration   i.clid #>          <char>       <char>       <char>       <char>      <num>   <char> #> 1:         <NA>         <NA>         <NA>         <NA>        168 CL129757 #> 2:         <NA>         <NA>         <NA>         <NA>        168 CL130742 #> 3:         <NA>         <NA>         <NA>         <NA>        168 CL131873 #> 4:         <NA>         <NA>         <NA>         <NA>        168 CL131903 #> 5:         <NA>         <NA>         <NA>         <NA>        168 CL130218 #> 6:         <NA>         <NA>         <NA>         <NA>        168 CL131438 #>    i.CellLineName i.Tissue i.parental_identifier i.subtype #>            <char>   <char>                <char>    <char> #> 1:          MCF-7   Breast                 MCF-7   unknown #> 2:          T-47D   Breast                 T-47D   unknown #> 3:        HCC1428   Breast               HCC1428   unknown #> 4:         BT-483   Breast                BT-483   unknown #> 5:         BT-474   Breast                BT-474   unknown #> 6:         CAMA-1   Breast                CAMA-1   unknown #>    i.ReferenceDivisionTime #>                      <num> #> 1:                      30 #> 2:                      60 #> 3:                      74 #> 4:                     130 #> 5:                      70 #> 6:                      53 #>  #> $CIScore_80 #> Key: <treatmentid, sampleid> #>    treatmentid sampleid drug_moa drug_moa_2 drug_moa_3 DrugName DrugName_2 #>         <char>   <char>   <char>     <char>     <char>   <char>     <char> #> 1:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 2:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 3:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 4:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 5:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 6:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #>    DrugName_3 Duration Gnumber Gnumber_2 CellLineName   clid #>        <char>    <num>  <char>    <char>       <char> <char> #> 1:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 2:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 3:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 4:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 5:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 6:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #>    parental_identifier ReferenceDivisionTime subtype Tissue    data_type #>                 <char>                 <num>  <char> <char>       <char> #> 1:                <NA>                    NA    <NA>   <NA> single-agent #> 2:                <NA>                    NA    <NA>   <NA> single-agent #> 3:                <NA>                    NA    <NA>   <NA> single-agent #> 4:                <NA>                    NA    <NA>   <NA> single-agent #> 5:                <NA>                    NA    <NA>   <NA> single-agent #> 6:                <NA>                    NA    <NA>   <NA> single-agent #>    normalization_type      x i.Gnumber  i.DrugName i.drug_moa i.Gnumber_2 #>                <char> <lgcl>    <char>      <char>     <char>      <char> #> 1:               <NA>     NA G02001876 Palbociclib  CDK4|CDK6        <NA> #> 2:               <NA>     NA G02001876 Palbociclib  CDK4|CDK6        <NA> #> 3:               <NA>     NA G02001876 Palbociclib  CDK4|CDK6        <NA> #> 4:               <NA>     NA G02001876 Palbociclib  CDK4|CDK6        <NA> #> 5:               <NA>     NA G02967907    GDC-0077     PI3K-A        <NA> #> 6:               <NA>     NA G02967907    GDC-0077     PI3K-A        <NA> #>    i.DrugName_2 i.drug_moa_2 i.DrugName_3 i.drug_moa_3 i.Duration   i.clid #>          <char>       <char>       <char>       <char>      <num>   <char> #> 1:         <NA>         <NA>         <NA>         <NA>        168 CL129757 #> 2:         <NA>         <NA>         <NA>         <NA>        168 CL130742 #> 3:         <NA>         <NA>         <NA>         <NA>        168 CL131873 #> 4:         <NA>         <NA>         <NA>         <NA>        168 CL131903 #> 5:         <NA>         <NA>         <NA>         <NA>        168 CL130218 #> 6:         <NA>         <NA>         <NA>         <NA>        168 CL131438 #>    i.CellLineName i.Tissue i.parental_identifier i.subtype #>            <char>   <char>                <char>    <char> #> 1:          MCF-7   Breast                 MCF-7   unknown #> 2:          T-47D   Breast                 T-47D   unknown #> 3:        HCC1428   Breast               HCC1428   unknown #> 4:         BT-483   Breast                BT-483   unknown #> 5:         BT-474   Breast                BT-474   unknown #> 6:         CAMA-1   Breast                CAMA-1   unknown #>    i.ReferenceDivisionTime #>                      <num> #> 1:                      30 #> 2:                      60 #> 3:                      74 #> 4:                     130 #> 5:                      70 #> 6:                      53 #>  #> $Metrics #> Key: <treatmentid, sampleid> #>    treatmentid sampleid drug_moa drug_moa_2 drug_moa_3 DrugName DrugName_2 #>         <char>   <char>   <char>     <char>     <char>   <char>     <char> #> 1:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 2:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 3:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 4:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 5:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #> 6:        <NA>     <NA>     <NA>       <NA>       <NA>     <NA>       <NA> #>    DrugName_3 Duration Gnumber Gnumber_2 CellLineName   clid #>        <char>    <num>  <char>    <char>       <char> <char> #> 1:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 2:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 3:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 4:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 5:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #> 6:       <NA>       NA    <NA>      <NA>         <NA>   <NA> #>    parental_identifier ReferenceDivisionTime subtype Tissue    data_type #>                 <char>                 <num>  <char> <char>       <char> #> 1:                <NA>                    NA    <NA>   <NA> single-agent #> 2:                <NA>                    NA    <NA>   <NA> single-agent #> 3:                <NA>                    NA    <NA>   <NA> single-agent #> 4:                <NA>                    NA    <NA>   <NA> single-agent #> 5:                <NA>                    NA    <NA>   <NA> single-agent #> 6:                <NA>                    NA    <NA>   <NA> single-agent #>       x_mean     x_AOC x_AOC_range       xc50    x_max       ec50      x_inf #>        <num>     <num>       <num>      <num>    <num>      <num>      <num> #> 1: 0.4766169 0.5233831   0.5685724 0.07649828 0.107050 0.06354470 0.08684205 #> 2: 0.6438030 0.3561970   0.3828886 0.26119890 0.281750 0.09897928 0.32080324 #> 3: 0.5797408 0.4202592   0.4560827 0.10802210 0.207125 0.08784832 0.21933259 #> 4: 0.4888085 0.5111915   0.5620006 0.06629065 0.111625 0.05911087 0.12311310 #> 5: 0.6458536 0.3541464   0.3770687 0.26781723 0.228300 0.13626047 0.27577126 #> 6: 0.4821213 0.5178787   0.5639825 0.06294109 0.148225 0.04029515 0.16592442 #>      x_0         h        r2   x_sd_avg               fit_type #>    <num>     <num>     <num>      <num>                 <char> #> 1:     1 1.0283168 0.9853800 0.05272629 DRC3pHillFitModelFixS0 #> 2:     1 1.0574543 0.9465590 0.07259453 DRC3pHillFitModelFixS0 #> 3:     1 2.7932767 0.9787945 0.06655135 DRC3pHillFitModelFixS0 #> 4:     1 2.4657832 0.9946671 0.07915584 DRC3pHillFitModelFixS0 #> 5:     1 1.1867664 0.9616801 0.06463053 DRC3pHillFitModelFixS0 #> 6:     1 0.9041923 0.9740112 0.05594059 DRC3pHillFitModelFixS0 #>    maxlog10Concentration N_conc normalization_type fit_source cotrt_value #>                    <num>  <int>             <char>     <char>       <num> #> 1:                     1     10                 RV        gDR          NA #> 2:                     1     10                 RV        gDR          NA #> 3:                     1     10                 RV        gDR          NA #> 4:                     1     10                 RV        gDR          NA #> 5:                     1     10                 RV        gDR          NA #> 6:                     1     10                 RV        gDR          NA #>    source i.Gnumber  i.DrugName i.drug_moa i.Gnumber_2 i.DrugName_2 #>    <char>    <char>      <char>     <char>      <char>       <char> #> 1:   <NA> G02001876 Palbociclib  CDK4|CDK6        <NA>         <NA> #> 2:   <NA> G02001876 Palbociclib  CDK4|CDK6        <NA>         <NA> #> 3:   <NA> G02001876 Palbociclib  CDK4|CDK6        <NA>         <NA> #> 4:   <NA> G02001876 Palbociclib  CDK4|CDK6        <NA>         <NA> #> 5:   <NA> G02001876 Palbociclib  CDK4|CDK6        <NA>         <NA> #> 6:   <NA> G02001876 Palbociclib  CDK4|CDK6        <NA>         <NA> #>    i.drug_moa_2 i.DrugName_3 i.drug_moa_3 i.Duration   i.clid i.CellLineName #>          <char>       <char>       <char>      <num>   <char>         <char> #> 1:         <NA>         <NA>         <NA>        168 CL129757          MCF-7 #> 2:         <NA>         <NA>         <NA>        168 CL130218         BT-474 #> 3:         <NA>         <NA>         <NA>        168 CL130742          T-47D #> 4:         <NA>         <NA>         <NA>        168 CL131438         CAMA-1 #> 5:         <NA>         <NA>         <NA>        168 CL131873        HCC1428 #> 6:         <NA>         <NA>         <NA>        168 CL131891         EFM-19 #>    i.Tissue i.parental_identifier i.subtype i.ReferenceDivisionTime #>      <char>                <char>    <char>                   <num> #> 1:   Breast                 MCF-7   unknown                      30 #> 2:   Breast                BT-474   unknown                      70 #> 3:   Breast                 T-47D   unknown                      60 #> 4:   Breast                CAMA-1   unknown                      53 #> 5:   Breast               HCC1428   unknown                      74 #> 6:   Breast                EFM-19   unknown                      64 assayNames(tre) #>  [1] \"RawTreated\"     \"Controls\"       \"Normalized\"     \"Averaged\"       #>  [5] \"SmoothMatrix\"   \"BlissExcess\"    \"HSAExcess\"      \"all_iso_points\" #>  [9] \"isobolograms\"   \"BlissScore\"     \"HSAScore\"       \"CIScore_50\"     #> [13] \"CIScore_80\"     \"Metrics\" head(assay(tre, \"Metrics\"),3) #> Key: <treatmentid, sampleid> #>                            treatmentid                                 sampleid #>                                 <char>                                   <char> #> 1: G02001876_Palbociclib_CDK4|CDK6_168   CL129757_MCF-7_Breast_MCF-7_unknown_30 #> 2: G02001876_Palbociclib_CDK4|CDK6_168 CL130218_BT-474_Breast_BT-474_unknown_70 #> 3: G02001876_Palbociclib_CDK4|CDK6_168   CL130742_T-47D_Breast_T-47D_unknown_60 #>     drug_moa drug_moa_2 drug_moa_3    DrugName DrugName_2 DrugName_3 Duration #>       <char>     <char>     <char>      <char>     <char>     <char>    <num> #> 1: CDK4|CDK6       <NA>       <NA> Palbociclib       <NA>       <NA>      168 #> 2: CDK4|CDK6       <NA>       <NA> Palbociclib       <NA>       <NA>      168 #> 3: CDK4|CDK6       <NA>       <NA> Palbociclib       <NA>       <NA>      168 #>      Gnumber Gnumber_2 CellLineName     clid parental_identifier #>       <char>    <char>       <char>   <char>              <char> #> 1: G02001876      <NA>        MCF-7 CL129757               MCF-7 #> 2: G02001876      <NA>       BT-474 CL130218              BT-474 #> 3: G02001876      <NA>        T-47D CL130742               T-47D #>    ReferenceDivisionTime subtype Tissue    data_type    x_mean     x_AOC #>                    <num>  <char> <char>       <char>     <num>     <num> #> 1:                    30 unknown Breast single-agent 0.4774514 0.5225486 #> 2:                    70 unknown Breast single-agent 0.5916887 0.4083113 #> 3:                    60 unknown Breast single-agent 0.5478704 0.4521296 #>    x_AOC_range      xc50     x_max      ec50       x_inf   x_0         h #>          <num>     <num>     <num>     <num>       <num> <num>     <num> #> 1:   0.5592516 0.1100133 -0.017025 0.1161741 -0.03117468     1 1.1100114 #> 2:   0.4338082 0.2091202  0.114275 0.1360264  0.16571556     1 0.9361851 #> 3:   0.4876840 0.1164343  0.111425 0.1033672  0.13053185     1 2.5415386 #>           r2   x_sd_avg               fit_type maxlog10Concentration N_conc #>        <num>      <num>                 <char>                 <num>  <int> #> 1: 0.9880388 0.05887778 DRC3pHillFitModelFixS0                     1     10 #> 2: 0.9555750 0.08197778 DRC3pHillFitModelFixS0                     1     10 #> 3: 0.9815621 0.06581980 DRC3pHillFitModelFixS0                     1     10 #>    normalization_type fit_source cotrt_value source i.Gnumber  i.DrugName #>                <char>     <char>       <num> <char>    <char>      <char> #> 1:                 GR        gDR          NA   <NA> G02001876 Palbociclib #> 2:                 GR        gDR          NA   <NA> G02001876 Palbociclib #> 3:                 GR        gDR          NA   <NA> G02001876 Palbociclib #>    i.drug_moa i.Gnumber_2 i.DrugName_2 i.drug_moa_2 i.DrugName_3 i.drug_moa_3 #>        <char>      <char>       <char>       <char>       <char>       <char> #> 1:  CDK4|CDK6        <NA>         <NA>         <NA>         <NA>         <NA> #> 2:  CDK4|CDK6        <NA>         <NA>         <NA>         <NA>         <NA> #> 3:  CDK4|CDK6        <NA>         <NA>         <NA>         <NA>         <NA> #>    i.Duration   i.clid i.CellLineName i.Tissue i.parental_identifier i.subtype #>         <num>   <char>         <char>   <char>                <char>    <char> #> 1:        168 CL129757          MCF-7   Breast                 MCF-7   unknown #> 2:        168 CL130218         BT-474   Breast                BT-474   unknown #> 3:        168 CL130742          T-47D   Breast                 T-47D   unknown #>    i.ReferenceDivisionTime #>                      <num> #> 1:                      30 #> 2:                      70 #> 3:                      60"},{"path":"https://gdrplatform.github.io/gDRimport/articles/ConvertingMAEtoPharmacoSet.html","id":"references","dir":"Articles","previous_headings":"","what":"References","title":"Converting a gDR-generated MultiAssayExperiment object into a PharmacoSet","text":"Song, K. W., Edgar, K. ., Hanan, E. J., Hafner, M., Oeh, J., Merchant, M., … & Friedman, L. S. (2022). RTK-dependent inducible degradation mutant PI3K drives GDC-0077 (Inavolisib) efficacy. Cancer discovery, 12(1), 204-219.","code":"sessionInfo() #> R version 4.3.0 (2023-04-21) #> Platform: x86_64-pc-linux-gnu (64-bit) #> Running under: Ubuntu 22.04.3 LTS #>  #> Matrix products: default #> BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3  #> LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;  LAPACK version 3.10.0 #>  #> locale: #>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               #>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     #>  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8    #>  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  #>  [9] LC_ADDRESS=C               LC_TELEPHONE=C             #> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C        #>  #> time zone: Etc/UTC #> tzcode source: system (glibc) #>  #> attached base packages: #> [1] stats4    stats     graphics  grDevices utils     datasets  methods   #> [8] base      #>  #> other attached packages: #>  [1] MultiAssayExperiment_1.28.0 gDRimport_1.5.3             #>  [3] PharmacoGx_3.6.0            CoreGx_2.6.1                #>  [5] SummarizedExperiment_1.32.0 Biobase_2.62.0              #>  [7] GenomicRanges_1.54.1        GenomeInfoDb_1.38.8         #>  [9] IRanges_2.36.0              S4Vectors_0.40.2            #> [11] MatrixGenerics_1.14.0       matrixStats_1.4.1           #> [13] BiocGenerics_0.48.1         #>  #> loaded via a namespace (and not attached): #>   [1] bitops_1.0-9            rlang_1.1.4             magrittr_2.0.3          #>   [4] shinydashboard_0.7.2    compiler_4.3.0          reshape2_1.4.4          #>   [7] maps_3.4.2.1            systemfonts_1.0.5       vctrs_0.6.5             #>  [10] relations_0.6-14        stringr_1.5.1           pkgconfig_2.0.3         #>  [13] crayon_1.5.3            fastmap_1.2.0           backports_1.5.0         #>  [16] XVector_0.42.0          caTools_1.18.3          utf8_1.2.4              #>  [19] promises_1.3.2          rmarkdown_2.29          pracma_2.4.4            #>  [22] ragg_1.2.7              magicaxis_2.4.5         coop_0.6-3              #>  [25] purrr_1.0.2             xfun_0.49               zlibbioc_1.48.2         #>  [28] cachem_1.1.0            celestial_1.4.6         jsonlite_1.8.9          #>  [31] SnowballC_0.7.1         later_1.4.1             DelayedArray_0.28.0     #>  [34] BiocParallel_1.36.0     parallel_4.3.0          sets_1.0-25             #>  [37] cluster_2.1.4           R6_2.5.1                stringi_1.8.4           #>  [40] bslib_0.8.0             RColorBrewer_1.1-3      qs_0.27.2               #>  [43] limma_3.58.1            boot_1.3-28.1           jquerylib_0.1.4         #>  [46] Rcpp_1.0.13-1           knitr_1.49              downloader_0.4          #>  [49] httpuv_1.6.15           Matrix_1.6-5            igraph_2.1.2            #>  [52] tidyselect_1.2.1        abind_1.4-8             yaml_2.3.10             #>  [55] stringfish_0.16.0       gplots_3.2.0            codetools_0.2-19        #>  [58] plyr_1.8.9              lattice_0.21-8          tibble_3.2.1            #>  [61] shiny_1.9.1             BumpyMatrix_1.10.0      evaluate_1.0.1          #>  [64] desc_1.4.3              RcppParallel_5.1.7      bench_1.1.3             #>  [67] pillar_1.9.0            lsa_0.73.3              KernSmooth_2.23-20      #>  [70] sm_2.2-6.0              checkmate_2.3.2         DT_0.33                 #>  [73] shinyjs_2.1.0           piano_2.18.0            generics_0.1.3          #>  [76] RCurl_1.98-1.16         ggplot2_3.5.1           munsell_0.5.1           #>  [79] scales_1.3.0            RApiSerialize_0.1.4     gtools_3.9.5            #>  [82] xtable_1.8-4            marray_1.80.0           glue_1.8.0              #>  [85] slam_0.1-55             mapproj_1.2.11          tools_4.3.0             #>  [88] data.table_1.16.4       gDRutils_1.5.3          fgsea_1.28.0            #>  [91] RANN_2.6.2              fs_1.6.5                visNetwork_2.1.2        #>  [94] fastmatch_1.1-4         cowplot_1.1.3           grid_4.3.0              #>  [97] plotrix_3.8-4           NISTunits_1.0.1         colorspace_2.1-1        #> [100] GenomeInfoDbData_1.2.11 cli_3.6.3               textshaping_0.3.7       #> [103] fansi_1.0.6             S4Arrays_1.2.1          dplyr_1.1.4             #> [106] gtable_0.3.6            sass_0.4.9              digest_0.6.37           #> [109] SparseArray_1.2.4       htmlwidgets_1.6.4       memoise_2.0.1           #> [112] htmltools_0.5.8.1       pkgdown_2.0.7           lifecycle_1.0.4         #> [115] statmod_1.5.0           mime_0.12               MASS_7.3-58.4"},{"path":"https://gdrplatform.github.io/gDRimport/articles/ConvertingPharmacoSetToGDR.html","id":"overview","dir":"Articles","previous_headings":"","what":"Overview","title":"Converting PharmacoSet Drug Response Data into gDR object","text":"gDRimport package part gDR suite. helps prepare raw drug response data downstream processing. mainly contains helper functions importing/loading/validating dose response data provided different scanner sources. collaboration BHKLab, gDRimport also provides functions can convert PharmacoGx::PharamcoSet object gDR object. functionality, users familiar gDR suite packages methods can utilize publically available, curated datasets PharmacoGx database. main step process extract drug dose-response data PharmacoSets transform data.table can used input gDRcore::runDrugResponseProcessingPipeline.","code":""},{"path":"https://gdrplatform.github.io/gDRimport/articles/ConvertingPharmacoSetToGDR.html","id":"loading-a-pharmacoset-pset","dir":"Articles","previous_headings":"","what":"Loading a PharmacoSet (PSet)","title":"Converting PharmacoSet Drug Response Data into gDR object","text":"Whereas user might already pharmacoset loaded R session, wish obtain different pharmacoset use script future provide helper function . helps user directory store pharmacosets, passing directory function parameter, function also check see PSet exists user-defined directory. ensure PSet re-downloaded already .","code":"pset <- getPSet(\"Tavor_2020\") pset"},{"path":"https://gdrplatform.github.io/gDRimport/articles/ConvertingPharmacoSetToGDR.html","id":"converting-pharmacoset-to-data-table-for-gdr-pipeline","dir":"Articles","previous_headings":"","what":"Converting PharmacoSet to data.table for gDR pipeline","title":"Converting PharmacoSet Drug Response Data into gDR object","text":"PharamcoSets hold data pertaining cell lines (@sample slot), drugs (@treatment slot), dose response experiments (@treatmentResponse slot). dose response data stored treatmentResponseExperiment object function gDRimport::convert_pset_to_df extracts information build data.table can used input gDR pipeline.","code":"# Store treatment response data in df_  dt <- convert_pset_to_df(pharmacoset = pset) str(dt) #> Classes 'data.table' and 'data.frame':   34516 obs. of  7 variables: #>  $ Barcode              : chr  \"PCM-0103090_1_130695_2018-08-28\" \"PCM-0103090_1_130695_2018-08-28\" \"PCM-0103090_1_130695_2018-08-28\" \"PCM-0103090_1_130695_2018-08-28\" ... #>  $ ReadoutValue         : num  75.7 63.1 75.9 87.2 78.8 ... #>  $ Concentration        : num  0.0021 0.0052 0.01 0.0299 0.0798 ... #>  $ Clid                 : chr  \"130695\" \"130695\" \"130695\" \"130695\" ... #>  $ DrugName             : chr  \"Ivosidenib\" \"Ivosidenib\" \"Ivosidenib\" \"Ivosidenib\" ... #>  $ Duration             : num  48 48 48 48 48 48 48 48 48 48 ... #>  $ ReferenceDivisionTime: logi  NA NA NA NA NA NA ... #>  - attr(*, \".internal.selfref\")=<externalptr>"},{"path":"https://gdrplatform.github.io/gDRimport/articles/ConvertingPharmacoSetToGDR.html","id":"subsetting-to-extract-relevant-information","dir":"Articles","previous_headings":"","what":"Subsetting to extract relevant information","title":"Converting PharmacoSet Drug Response Data into gDR object","text":"canonical PharmacoSets data pertaining many cell lines response many drugs (drug-combination data available conversion gDR currently supported). , interest time resources, may useful subset data providing input gDR pipeline.","code":"# example subset using only 1 cell line subset_cl <- dt$Clid[1] x <- dt[Clid == subset_cl] x #>                              Barcode ReadoutValue Concentration   Clid #>                               <char>        <num>         <num> <char> #>   1: PCM-0103090_1_130695_2018-08-28       75.733        0.0021 130695 #>   2: PCM-0103090_1_130695_2018-08-28       63.094        0.0052 130695 #>   3: PCM-0103090_1_130695_2018-08-28       75.935        0.0100 130695 #>   4: PCM-0103090_1_130695_2018-08-28       87.159        0.0299 130695 #>   5: PCM-0103090_1_130695_2018-08-28       78.766        0.0798 130695 #>  ---                                                                   #> 589: PCM-0064526_5_130695_2018-08-28       71.707        1.4960 130695 #> 590: PCM-0064526_5_130695_2018-08-28       60.488        3.9900 130695 #> 591: PCM-0064526_5_130695_2018-08-28       25.366        9.9750 130695 #> 592: PCM-0064526_5_130695_2018-08-28        5.976       24.9400 130695 #> 593: PCM-0064526_5_130695_2018-08-28      100.000        0.0000 130695 #>         DrugName Duration ReferenceDivisionTime #>           <char>    <num>                <lgcl> #>   1:  Ivosidenib       48                    NA #>   2:  Ivosidenib       48                    NA #>   3:  Ivosidenib       48                    NA #>   4:  Ivosidenib       48                    NA #>   5:  Ivosidenib       48                    NA #>  ---                                            #> 589: Azacitidine       48                    NA #> 590: Azacitidine       48                    NA #> 591: Azacitidine       48                    NA #> 592: Azacitidine       48                    NA #> 593:     vehicle       48                    NA"},{"path":"https://gdrplatform.github.io/gDRimport/articles/ConvertingPharmacoSetToGDR.html","id":"running-drug-response-pipeline-with-data","dir":"Articles","previous_headings":"","what":"Running drug response pipeline with data","title":"Converting PharmacoSet Drug Response Data into gDR object","text":"subsetted data can now used input gDRcore::runDrugResponseProcessingPipeline(). output function MultiAssayExperiment object can accessed gDRutils::convert_se_assay_to_dt()","code":"# RUN DRUG RESPONSE PROCESSING PIPELINE se <- gDRcore::runDrugResponseProcessingPipeline(x) se # Convert Summarized Experiments to data.table  # Available SEs : \"RawTreatred\", \"Controls\", \"Normalized\", \"Averaged\", \"Metrics\"  str(gDRutils::convert_se_assay_to_dt(se[[1]], \"Averaged\")) str(gDRutils::convert_se_assay_to_dt(se[[1]], \"Metrics\"))"},{"path":"https://gdrplatform.github.io/gDRimport/articles/ConvertingPharmacoSetToGDR.html","id":"sessioninfo","dir":"Articles","previous_headings":"","what":"SessionInfo","title":"Converting PharmacoSet Drug Response Data into gDR object","text":"","code":"sessionInfo() #> R version 4.3.0 (2023-04-21) #> Platform: x86_64-pc-linux-gnu (64-bit) #> Running under: Ubuntu 22.04.3 LTS #>  #> Matrix products: default #> BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3  #> LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;  LAPACK version 3.10.0 #>  #> locale: #>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               #>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     #>  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8    #>  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  #>  [9] LC_ADDRESS=C               LC_TELEPHONE=C             #> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C        #>  #> time zone: Etc/UTC #> tzcode source: system (glibc) #>  #> attached base packages: #> [1] stats4    stats     graphics  grDevices utils     datasets  methods   #> [8] base      #>  #> other attached packages: #>  [1] gDRimport_1.5.3             PharmacoGx_3.6.0            #>  [3] CoreGx_2.6.1                SummarizedExperiment_1.32.0 #>  [5] Biobase_2.62.0              GenomicRanges_1.54.1        #>  [7] GenomeInfoDb_1.38.8         IRanges_2.36.0              #>  [9] S4Vectors_0.40.2            MatrixGenerics_1.14.0       #> [11] matrixStats_1.4.1           BiocGenerics_0.48.1         #>  #> loaded via a namespace (and not attached): #>   [1] RColorBrewer_1.1-3          jsonlite_1.8.9              #>   [3] MultiAssayExperiment_1.28.0 magrittr_2.0.3              #>   [5] rmarkdown_2.29              fs_1.6.5                    #>   [7] zlibbioc_1.48.2             ragg_1.2.7                  #>   [9] vctrs_0.6.5                 memoise_2.0.1               #>  [11] magicaxis_2.4.5             RCurl_1.98-1.16             #>  [13] htmltools_0.5.8.1           S4Arrays_1.2.1              #>  [15] plotrix_3.8-4               SparseArray_1.2.4           #>  [17] sass_0.4.9                  pracma_2.4.4                #>  [19] KernSmooth_2.23-20          bslib_0.8.0                 #>  [21] htmlwidgets_1.6.4           desc_1.4.3                  #>  [23] plyr_1.8.9                  testthat_3.2.1              #>  [25] cachem_1.1.0                igraph_2.1.2                #>  [27] mime_0.12                   lifecycle_1.0.4             #>  [29] piano_2.18.0                pkgconfig_2.0.3             #>  [31] Matrix_1.6-5                R6_2.5.1                    #>  [33] fastmap_1.2.0               GenomeInfoDbData_1.2.11     #>  [35] shiny_1.9.1                 digest_0.6.37               #>  [37] colorspace_2.1-1            rprojroot_2.0.4             #>  [39] pkgload_1.3.4               textshaping_0.3.7           #>  [41] SnowballC_0.7.1             fansi_1.0.6                 #>  [43] abind_1.4-8                 coop_0.6-3                  #>  [45] compiler_4.3.0              downloader_0.4              #>  [47] marray_1.80.0               backports_1.5.0             #>  [49] BiocParallel_1.36.0         gDRutils_1.5.3              #>  [51] bench_1.1.3                 qs_0.27.2                   #>  [53] gplots_3.2.0                maps_3.4.2.1                #>  [55] MASS_7.3-58.4               DelayedArray_0.28.0         #>  [57] gtools_3.9.5                caTools_1.18.3              #>  [59] tools_4.3.0                 NISTunits_1.0.1             #>  [61] httpuv_1.6.15               relations_0.6-14            #>  [63] glue_1.8.0                  promises_1.3.2              #>  [65] grid_4.3.0                  checkmate_2.3.2             #>  [67] cluster_2.1.4               reshape2_1.4.4              #>  [69] fgsea_1.28.0                generics_0.1.3              #>  [71] gtable_0.3.6                sm_2.2-6.0                  #>  [73] data.table_1.16.4           RApiSerialize_0.1.4         #>  [75] stringfish_0.16.0           utf8_1.2.4                  #>  [77] XVector_0.42.0              RANN_2.6.2                  #>  [79] pillar_1.9.0                stringr_1.5.1               #>  [81] limma_3.58.1                BumpyMatrix_1.10.0          #>  [83] later_1.4.1                 dplyr_1.1.4                 #>  [85] lattice_0.21-8              tidyselect_1.2.1            #>  [87] knitr_1.49                  xfun_0.49                   #>  [89] shinydashboard_0.7.2        statmod_1.5.0               #>  [91] brio_1.1.4                  DT_0.33                     #>  [93] visNetwork_2.1.2            stringi_1.8.4               #>  [95] yaml_2.3.10                 boot_1.3-28.1               #>  [97] evaluate_1.0.1              codetools_0.2-19            #>  [99] lsa_0.73.3                  tibble_3.2.1                #> [101] cli_3.6.3                   RcppParallel_5.1.7          #> [103] xtable_1.8-4                systemfonts_1.0.5           #> [105] munsell_0.5.1               jquerylib_0.1.4             #> [107] Rcpp_1.0.13-1               mapproj_1.2.11              #> [109] parallel_4.3.0              sets_1.0-25                 #> [111] pkgdown_2.0.7               ggplot2_3.5.1               #> [113] assertthat_0.2.1            bitops_1.0-9                #> [115] slam_0.1-55                 celestial_1.4.6             #> [117] scales_1.3.0                purrr_1.0.2                 #> [119] crayon_1.5.3                rlang_1.1.4                 #> [121] cowplot_1.1.3               fastmatch_1.1-4             #> [123] shinyjs_2.1.0"},{"path":"https://gdrplatform.github.io/gDRimport/articles/gDRimport.html","id":"overview","dir":"Articles","previous_headings":"","what":"Overview","title":"gDRimport","text":"gDRimport package part gDR suite. helps prepare raw drug response data downstream processing. mainly contains helper functions importing/loading/validating dose response data provided different file formats.","code":""},{"path":[]},{"path":"https://gdrplatform.github.io/gDRimport/articles/gDRimport.html","id":"test-data","dir":"Articles","previous_headings":"Use Cases","what":"Test Data","title":"gDRimport","text":"currently four test datasets can used see ’s expected input data gDRimport.","code":"# primary test data td1 <- get_test_data() summary(td1) ##        Length         Class          Mode  ##             1 gdr_test_data            S4 td1 ## class: gdr_test_data  ## slots: manifest_path result_path template_path ref_m_df ref_r1_r2 ref_r1 ref_t1_t2 ref_t1 # test data in Tecan format td2 <- get_test_Tecan_data() summary(td2) ##          Length Class  Mode      ## m_file   1      -none- character ## r_files  1      -none- character ## t_files  1      -none- character ## ref_m_df 1      -none- character ## ref_r_df 1      -none- character ## ref_t_df 1      -none- character # test data in D300 format td3 <- get_test_D300_data() summary(td3) ##        Length Class  Mode ## f_96w  6      -none- list ## f_384w 6      -none- list # test data obtained from EnVision td4 <- get_test_EnVision_data() summary(td4) ##            Length Class  Mode      ## m_file      1     -none- character ## r_files    28     -none- character ## t_files     2     -none- character ## ref_l_path  1     -none- character"},{"path":"https://gdrplatform.github.io/gDRimport/articles/gDRimport.html","id":"load-data","dir":"Articles","previous_headings":"Use Cases","what":"Load data","title":"gDRimport","text":"load_data key function. wraps load_manifest, load_templates load_results functions supports different file formats.","code":"ml <- load_manifest(manifest_path(td1)) summary(ml) ##         Length Class      Mode ## data     4     data.table list ## headers 27     -none-     list t_df <- load_templates(template_path(td1)) summary(t_df) ##    WellRow           WellColumn          Gnumber          Concentration      ##  Length:768         Length:768         Length:768         Length:768         ##  Class :character   Class :character   Class :character   Class :character   ##  Mode  :character   Mode  :character   Mode  :character   Mode  :character   ##   Gnumber_2         Concentration_2      Template         ##  Length:768         Length:768         Length:768         ##  Class :character   Class :character   Class :character   ##  Mode  :character   Mode  :character   Mode  :character r_df <- suppressMessages(load_results(result_path(td1))) summary(r_df) ##    Barcode            WellRow            WellColumn     ReadoutValue     ##  Length:4587        Length:4587        Min.   : 1.00   Min.   :  12627   ##  Class :character   Class :character   1st Qu.: 6.50   1st Qu.:  67905   ##  Mode  :character   Mode  :character   Median :12.00   Median : 140865   ##                                        Mean   :12.49   Mean   : 263996   ##                                        3rd Qu.:18.00   3rd Qu.: 324707   ##                                        Max.   :24.00   Max.   :2423054   ##  BackgroundValue ##  Min.   :332.0   ##  1st Qu.:351.0   ##  Median :374.0   ##  Mean   :453.2   ##  3rd Qu.:570.0   ##  Max.   :704.0 l_tbl <-   suppressMessages(     load_data(manifest_path(td1), template_path(td1), result_path(td1))) summary(l_tbl) ##            Length Class      Mode ## manifest   4      data.table list ## treatments 7      data.table list ## data       5      data.table list"},{"path":"https://gdrplatform.github.io/gDRimport/articles/gDRimport.html","id":"prism","dir":"Articles","previous_headings":"","what":"PRISM","title":"gDRimport","text":"PRISM, Multiplexed cancer cell line screening platform, facilitates rapid screening broad spectrum drugs across 900 human cancer cell line models, employing high-throughput, multiplexed approach. Publicly available PRISM data can downloaded DepMap website (DepMap). gDRimport package provides support processing PRISM data two levels: LEVEL5 LEVEL6. LEVEL5 Data: format encapsulates information drugs, cell lines, viability within single file. process LEVEL5 PRISM data, can use convert_LEVEL5_prism_to_gDR_input() function. function transforms cleans data also executes gDR pipeline analysis. LEVEL6 Data: LEVEL6, PRISM data distributed across three separate files: prism_data: containing collapsed log fold change data viability assays. cell_line_data: providing information cell lines. treatment_data: containing treatment data. Processing LEVEL6 PRISM data can accomplished using convert_LEVEL6_prism_to_gDR_input() function, requires paths three files input arguments.","code":""},{"path":"https://gdrplatform.github.io/gDRimport/articles/gDRimport.html","id":"processing-level5-prism-data","dir":"Articles","previous_headings":"PRISM","what":"Processing LEVEL5 PRISM Data","title":"gDRimport","text":"process LEVEL5 PRISM data, can use following function: Replace “path_to_file” actual path LEVEL5 PRISM data file. function handle transformation, cleaning, execution gDR pipeline automatically.","code":"convert_LEVEL5_prism_to_gDR_input(\"path_to_file\")"},{"path":"https://gdrplatform.github.io/gDRimport/articles/gDRimport.html","id":"processing-level6-prism-data","dir":"Articles","previous_headings":"PRISM","what":"Processing LEVEL6 PRISM Data","title":"gDRimport","text":"process LEVEL6 PRISM data, can use following function: Replace “prism_data_path”, “cell_line_data_path”, “treatment_data_path” respective paths LEVEL6 PRISM data files.","code":"convert_LEVEL6_prism_to_gDR_input(\"prism_data_path\", \"cell_line_data_path\", \"treatment_data_path\")"},{"path":"https://gdrplatform.github.io/gDRimport/articles/gDRimport.html","id":"package-installation","dir":"Articles","previous_headings":"PRISM","what":"Package installation","title":"gDRimport","text":"function installAllDeps assists installing package dependencies.","code":""},{"path":"https://gdrplatform.github.io/gDRimport/articles/gDRimport.html","id":"sessioninfo","dir":"Articles","previous_headings":"","what":"SessionInfo","title":"gDRimport","text":"","code":"sessionInfo() ## R version 4.3.0 (2023-04-21) ## Platform: x86_64-pc-linux-gnu (64-bit) ## Running under: Ubuntu 22.04.3 LTS ##  ## Matrix products: default ## BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3  ## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;  LAPACK version 3.10.0 ##  ## locale: ##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               ##  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     ##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8    ##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  ##  [9] LC_ADDRESS=C               LC_TELEPHONE=C             ## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C        ##  ## time zone: Etc/UTC ## tzcode source: system (glibc) ##  ## attached base packages: ## [1] stats     graphics  grDevices utils     datasets  methods   base      ##  ## other attached packages: ## [1] gDRimport_1.5.3  BiocStyle_2.30.0 ##  ## loaded via a namespace (and not attached): ##  [1] SummarizedExperiment_1.32.0 xfun_0.49                   ##  [3] bslib_0.8.0                 Biobase_2.62.0              ##  [5] lattice_0.21-8              vctrs_0.6.5                 ##  [7] tools_4.3.0                 bitops_1.0-9                ##  [9] stats4_4.3.0                tibble_3.2.1                ## [11] fansi_1.0.6                 pkgconfig_2.0.3             ## [13] Matrix_1.6-5                data.table_1.16.4           ## [15] checkmate_2.3.2             desc_1.4.3                  ## [17] S4Vectors_0.40.2            gDRutils_1.5.3              ## [19] rematch_2.0.0               readxl_1.4.3                ## [21] assertthat_0.2.1            lifecycle_1.0.4             ## [23] GenomeInfoDbData_1.2.11     compiler_4.3.0              ## [25] textshaping_0.3.7           GenomeInfoDb_1.38.8         ## [27] htmltools_0.5.8.1           sass_0.4.9                  ## [29] RCurl_1.98-1.16             yaml_2.3.10                 ## [31] pillar_1.9.0                pkgdown_2.0.7               ## [33] crayon_1.5.3                jquerylib_0.1.4             ## [35] DelayedArray_0.28.0         cachem_1.1.0                ## [37] abind_1.4-8                 digest_0.6.37               ## [39] purrr_1.0.2                 bookdown_0.37               ## [41] fastmap_1.2.0               grid_4.3.0                  ## [43] cli_3.6.3                   SparseArray_1.2.4           ## [45] magrittr_2.0.3              S4Arrays_1.2.1              ## [47] utf8_1.2.4                  backports_1.5.0             ## [49] rmarkdown_2.29              lambda.r_1.2.4              ## [51] XVector_0.42.0              matrixStats_1.4.1           ## [53] futile.logger_1.4.3         cellranger_1.1.0            ## [55] ragg_1.2.7                  memoise_2.0.1               ## [57] evaluate_1.0.1              knitr_1.49                  ## [59] GenomicRanges_1.54.1        IRanges_2.36.0              ## [61] rlang_1.1.4                 futile.options_1.0.1        ## [63] glue_1.8.0                  BiocManager_1.30.22         ## [65] formatR_1.14                BiocGenerics_0.48.1         ## [67] jsonlite_1.8.9              R6_2.5.1                    ## [69] MatrixGenerics_1.14.0       systemfonts_1.0.5           ## [71] fs_1.6.5                    zlibbioc_1.48.2"},{"path":"https://gdrplatform.github.io/gDRimport/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Arkadiusz Gladki. Author, maintainer. Bartosz Czech. Author. Marc Hafner. Author. Sergiu Mocanu. Author. Dariusz Scigocki. Author. Allison Vuong. Author. Luca Gerosa. Author. Janina Smola. Author.","code":""},{"path":"https://gdrplatform.github.io/gDRimport/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Gladki , Czech B, Hafner M, Mocanu S, Scigocki D, Vuong , Gerosa L, Smola J (2024). gDRimport: Package handling import dose-response data. https://github.com/gdrplatform/gDRimport, https://gdrplatform.github.io/gDRimport/.","code":"@Manual{,   title = {gDRimport: Package for handling the import of dose-response data},   author = {Arkadiusz Gladki and Bartosz Czech and Marc Hafner and Sergiu Mocanu and Dariusz Scigocki and Allison Vuong and Luca Gerosa and Janina Smola},   year = {2024},   note = {https://github.com/gdrplatform/gDRimport, https://gdrplatform.github.io/gDRimport/}, }"},{"path":"https://gdrplatform.github.io/gDRimport/index.html","id":"gdrimport","dir":"","previous_headings":"","what":"Package for handling the import of dose-response data","title":"Package for handling the import of dose-response data","text":"Package handling import dose-response data","code":""},{"path":"https://gdrplatform.github.io/gDRimport/index.html","id":"website","dir":"","previous_headings":"","what":"Website","title":"Package for handling the import of dose-response data","text":"package website available link.","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/are_template_sheets_valid.html","id":null,"dir":"Reference","previous_headings":"","what":"are template sheet valid? — are_template_sheets_valid","title":"are template sheet valid? — are_template_sheets_valid","text":"template sheet valid?","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/are_template_sheets_valid.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"are template sheet valid? — are_template_sheets_valid","text":"","code":"are_template_sheets_valid(ts)"},{"path":"https://gdrplatform.github.io/gDRimport/reference/are_template_sheets_valid.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"are template sheet valid? — are_template_sheets_valid","text":"ts list (per file) template sheets","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/are_template_sheets_valid.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"are template sheet valid? — are_template_sheets_valid","text":"logical flag","code":""},{"path":[]},{"path":"https://gdrplatform.github.io/gDRimport/reference/check_metadata_against_spaces.html","id":null,"dir":"Reference","previous_headings":"","what":"Check metadata against spaces — check_metadata_against_spaces","title":"Check metadata against spaces — check_metadata_against_spaces","text":"Check metadata spaces","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/check_metadata_against_spaces.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check metadata against spaces — check_metadata_against_spaces","text":"","code":"check_metadata_against_spaces(corrected_names, df_name)"},{"path":"https://gdrplatform.github.io/gDRimport/reference/check_metadata_against_spaces.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check metadata against spaces — check_metadata_against_spaces","text":"corrected_names charvec corrected colnames df df_name name data.table (\"\" default)","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/check_metadata_against_spaces.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check metadata against spaces — check_metadata_against_spaces","text":"charvec corrected colnames df","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/check_metadata_field_names.html","id":null,"dir":"Reference","previous_headings":"","what":"Check metadata field names — check_metadata_field_names","title":"Check metadata field names — check_metadata_field_names","text":"Check metadata field names","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/check_metadata_field_names.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check metadata field names — check_metadata_field_names","text":"","code":"check_metadata_field_names(corrected_names, df_name)"},{"path":"https://gdrplatform.github.io/gDRimport/reference/check_metadata_field_names.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check metadata field names — check_metadata_field_names","text":"corrected_names charvec corrected colnames df df_name name data.table (\"\" default)","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/check_metadata_field_names.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check metadata field names — check_metadata_field_names","text":"charvec corrected colnames df","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/check_metadata_headers.html","id":null,"dir":"Reference","previous_headings":"","what":"Check whether metadata headers are correct and make fixes if needed — check_metadata_headers","title":"Check whether metadata headers are correct and make fixes if needed — check_metadata_headers","text":"Check whether metadata headers correct make fixes needed","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/check_metadata_headers.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check whether metadata headers are correct and make fixes if needed — check_metadata_headers","text":"","code":"check_metadata_headers(corrected_names, df_name)"},{"path":"https://gdrplatform.github.io/gDRimport/reference/check_metadata_headers.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check whether metadata headers are correct and make fixes if needed — check_metadata_headers","text":"corrected_names charvec corrected colnames df df_name name data.table (\"\" default)","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/check_metadata_headers.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check whether metadata headers are correct and make fixes if needed — check_metadata_headers","text":"charvec corrected colnames df","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/check_metadata_names.html","id":null,"dir":"Reference","previous_headings":"","what":"check_metadata_names — check_metadata_names","title":"check_metadata_names — check_metadata_names","text":"Check whether metadata names correct","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/check_metadata_names.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"check_metadata_names — check_metadata_names","text":"","code":"check_metadata_names(col_df, df_name = \"\", df_type = NULL)"},{"path":"https://gdrplatform.github.io/gDRimport/reference/check_metadata_names.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"check_metadata_names — check_metadata_names","text":"col_df character colnames df df_name name data.table (\"\" default) df_type type data.table (NULL default)","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/check_metadata_names.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"check_metadata_names — check_metadata_names","text":"charvec corrected colnames df","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/check_metadata_names.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"check_metadata_names — check_metadata_names","text":"","code":"td <- get_test_data()  m_file <- manifest_path(td)  m_data <- read_excel_to_dt(m_file)  result <- check_metadata_names(col_df = colnames(m_data))"},{"path":"https://gdrplatform.github.io/gDRimport/reference/check_metadata_req_col_names.html","id":null,"dir":"Reference","previous_headings":"","what":"Check metadata for required column names — check_metadata_req_col_names","title":"Check metadata for required column names — check_metadata_req_col_names","text":"Check metadata required column names","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/check_metadata_req_col_names.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check metadata for required column names — check_metadata_req_col_names","text":"","code":"check_metadata_req_col_names(col_df, df_name, df_type)"},{"path":"https://gdrplatform.github.io/gDRimport/reference/check_metadata_req_col_names.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check metadata for required column names — check_metadata_req_col_names","text":"col_df charvec corrected colnames df df_name name data.table (\"\" default) df_type type data.table (NULL default)","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/check_metadata_req_col_names.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check metadata for required column names — check_metadata_req_col_names","text":"NULL invisibly.","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/convert_LEVEL5_prism_to_gDR_input.html","id":null,"dir":"Reference","previous_headings":"","what":"Load, convert and process the level 5 PRISM data into a gDR input — convert_LEVEL5_prism_to_gDR_input","title":"Load, convert and process the level 5 PRISM data into a gDR input — convert_LEVEL5_prism_to_gDR_input","text":"Load, convert process level 5 PRISM data gDR input","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/convert_LEVEL5_prism_to_gDR_input.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Load, convert and process the level 5 PRISM data into a gDR input — convert_LEVEL5_prism_to_gDR_input","text":"","code":"convert_LEVEL5_prism_to_gDR_input(prism_data_path, readout_min = 1.03)"},{"path":"https://gdrplatform.github.io/gDRimport/reference/convert_LEVEL5_prism_to_gDR_input.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Load, convert and process the level 5 PRISM data into a gDR input — convert_LEVEL5_prism_to_gDR_input","text":"prism_data_path path PRISM LEVEL5 csv file data readout_min minimum ReadoutValue","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/convert_LEVEL5_prism_to_gDR_input.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Load, convert and process the level 5 PRISM data into a gDR input — convert_LEVEL5_prism_to_gDR_input","text":"data.table object input data gDR pipeline","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/convert_LEVEL5_prism_to_gDR_input.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Load, convert and process the level 5 PRISM data into a gDR input — convert_LEVEL5_prism_to_gDR_input","text":"","code":"prism_data <- system.file(\"testdata/prism_sa.csv\", package = \"gDRimport\")  convert_LEVEL5_prism_to_gDR_input(prism_data) #>         clid Duration ReadoutValue BackgroundValue     Gnumber Concentration #>       <char>    <num>        <num>           <num>      <char>         <num> #> 1: some_clid      120         1.03               0 someGnumber      0.003201 #> 2: some_clid      120         1.00               0     vehicle      0.000000 #>    masked #>    <lgcl> #> 1:  FALSE #> 2:  FALSE"},{"path":"https://gdrplatform.github.io/gDRimport/reference/convert_LEVEL6_prism_to_gDR_input.html","id":null,"dir":"Reference","previous_headings":"","what":"Load, convert and process the level 6 PRISM data into a gDR input — convert_LEVEL6_prism_to_gDR_input","title":"Load, convert and process the level 6 PRISM data into a gDR input — convert_LEVEL6_prism_to_gDR_input","text":"Load, convert process level 6 PRISM data gDR input","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/convert_LEVEL6_prism_to_gDR_input.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Load, convert and process the level 6 PRISM data into a gDR input — convert_LEVEL6_prism_to_gDR_input","text":"","code":"convert_LEVEL6_prism_to_gDR_input(   prism_data_path,   cell_line_data_path,   treatment_data_path,   readout_min = 1.03 )"},{"path":"https://gdrplatform.github.io/gDRimport/reference/convert_LEVEL6_prism_to_gDR_input.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Load, convert and process the level 6 PRISM data into a gDR input — convert_LEVEL6_prism_to_gDR_input","text":"prism_data_path path PRISM LEVEL6 csv file collapsed log fold change data cell_line_data_path path cell line info data treatment_data_path path collapsed treatment info data readout_min minimum ReadoutValue","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/convert_LEVEL6_prism_to_gDR_input.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Load, convert and process the level 6 PRISM data into a gDR input — convert_LEVEL6_prism_to_gDR_input","text":"data.table object input data gDR pipeline","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/convert_LEVEL6_prism_to_gDR_input.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Load, convert and process the level 6 PRISM data into a gDR input — convert_LEVEL6_prism_to_gDR_input","text":"","code":"prism_data_path <- system.file(\"testdata/prism_collapsed_LOGFC.csv\", package = \"gDRimport\")  cell_line_data_path <- system.file(\"testdata/prism_cell_lines.csv\", package = \"gDRimport\")  treatment_data_path <- system.file(\"testdata/prism_treatment.csv\", package = \"gDRimport\")  convert_LEVEL6_prism_to_gDR_input(prism_data_path, cell_line_data_path, treatment_data_path) #>         clid        Gnumber       DrugName      drug_moa Duration Concentration #>       <char>         <char>         <char>        <char>    <num>         <num> #> 1: some_clid some_drug_name some_drug_name some_drug_moa      120      2.325889 #> 2: some_clid        vehicle        vehicle       vehicle      120      0.000000 #>    ReadoutValue masked #>           <num> <lgcl> #> 1:    0.9892612  FALSE #> 2:    1.0000000  FALSE"},{"path":"https://gdrplatform.github.io/gDRimport/reference/convert_MAE_to_PSet.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert MultiAssayExperiment to TreatmentResponseExperiment — convert_MAE_to_PSet","title":"Convert MultiAssayExperiment to TreatmentResponseExperiment — convert_MAE_to_PSet","text":"function converts MultiAssayExperiment generated gDR TreatmentResponseExperiment use PharmacoGx package. resulting PharmacoSet can used pharmacogenomic analysis drug response.","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/convert_MAE_to_PSet.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert MultiAssayExperiment to TreatmentResponseExperiment — convert_MAE_to_PSet","text":"","code":"convert_MAE_to_PSet(mae, pset_name)"},{"path":"https://gdrplatform.github.io/gDRimport/reference/convert_MAE_to_PSet.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert MultiAssayExperiment to TreatmentResponseExperiment — convert_MAE_to_PSet","text":"mae MultiAssayExperiment object generated gDR. pset_name character string specifying name resulting PharmacoSet object.","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/convert_MAE_to_PSet.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert MultiAssayExperiment to TreatmentResponseExperiment — convert_MAE_to_PSet","text":"PharmacoSet object.","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/convert_MAE_to_PSet.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Convert MultiAssayExperiment to TreatmentResponseExperiment — convert_MAE_to_PSet","text":"","code":"# Convert a MultiAssayExperiment object to a PharmacoSet object m <- 20 n <- 10 rnames <- LETTERS[1:m] cnames <- letters[1:n] ref_gr_value <-  matrix(runif(m * n), nrow = m, ncol = n, dimnames = list(rnames, cnames)) se <- SummarizedExperiment::SummarizedExperiment(assays = list(RefGRvalue = ref_gr_value),                                                  rowData = S4Vectors::DataFrame(rnames),                                                  colData = S4Vectors::DataFrame(cnames)) mae <- MultiAssayExperiment::MultiAssayExperiment(experiments = list(\"single-agent\" = se)) convert_MAE_to_PSet(mae, \"my_pset\") #> <PharmacoSet> #> Name:  my_pset  #> Date Created:  Mon Dec  9 10:53:08 2024  #> Number of samples:  10  #> Molecular profiles: #>    A MultiAssayExperiment object of 1 listed #>    experiment with a user-defined name and respective class. #>    Containing an ExperimentList class object of length 1: #>    [1] emptySE: SummarizedExperiment with 0 rows and 10 columns  #> Treatment response: #>    <TreatmentResponseExperiment>  #>   dim:  20 10  #>   assays(1): RefGRvalue  #>   rownames(20): A B ... S T  #>   rowData(2): treatmentid rnames  #>   colnames(10): a b c ... h i j  #>   colData(2): sampleid cnames  #>   metadata(0): none"},{"path":"https://gdrplatform.github.io/gDRimport/reference/convert_pset_to_df.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert a PharmacoSet to a data.table that is prepare for input into gDR pipeline — convert_pset_to_df","title":"Convert a PharmacoSet to a data.table that is prepare for input into gDR pipeline — convert_pset_to_df","text":"Convert PharmacoSet data.table prepare input gDR pipeline","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/convert_pset_to_df.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert a PharmacoSet to a data.table that is prepare for input into gDR pipeline — convert_pset_to_df","text":"","code":"convert_pset_to_df(pharmacoset, run_parallel = TRUE, workers = 2L)"},{"path":"https://gdrplatform.github.io/gDRimport/reference/convert_pset_to_df.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert a PharmacoSet to a data.table that is prepare for input into gDR pipeline — convert_pset_to_df","text":"pharmacoset PharmacoSet object run_parallel logical, TRUE (default) run functions Parallel, FALSE run serial workers integer, number workers defaults 2L run_parallel TRUE","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/convert_pset_to_df.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert a PharmacoSet to a data.table that is prepare for input into gDR pipeline — convert_pset_to_df","text":"data.table PharmacoSet's dose response data column names aligned gDR standard","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/convert_pset_to_df.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Convert a PharmacoSet to a data.table that is prepare for input into gDR pipeline — convert_pset_to_df","text":"Jermiah Joseph -- collaboration BHKLab","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/convert_pset_to_df.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Convert a PharmacoSet to a data.table that is prepare for input into gDR pipeline — convert_pset_to_df","text":"","code":"pset <- suppressMessages(getPSet(   \"Tavor_2020\",    psetDir = system.file(\"extdata/pset\", package = \"gDRimport\"),   use_local_PSets_list = TRUE )) dt <- convert_pset_to_df(pset) gDRutils::reset_env_identifiers()"},{"path":"https://gdrplatform.github.io/gDRimport/reference/correct_template_sheets.html","id":null,"dir":"Reference","previous_headings":"","what":"Correct names of the template sheets (if required) — correct_template_sheets","title":"Correct names of the template sheets (if required) — correct_template_sheets","text":"Correct names template sheets (required)","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/correct_template_sheets.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Correct names of the template sheets (if required) — correct_template_sheets","text":"","code":"correct_template_sheets(tfiles)"},{"path":"https://gdrplatform.github.io/gDRimport/reference/correct_template_sheets.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Correct names of the template sheets (if required) — correct_template_sheets","text":"tfiles charvec paths template files","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/correct_template_sheets.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Correct names of the template sheets (if required) — correct_template_sheets","text":"charvec paths corrected sheet names","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/detect_file_format.html","id":null,"dir":"Reference","previous_headings":"","what":"Detect format of results data — detect_file_format","title":"Detect format of results data — detect_file_format","text":"Detect format results data","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/detect_file_format.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Detect format of results data — detect_file_format","text":"","code":"detect_file_format(results_file)"},{"path":"https://gdrplatform.github.io/gDRimport/reference/detect_file_format.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Detect format of results data — detect_file_format","text":"results_file path results data","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/detect_file_format.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Detect format of results data — detect_file_format","text":"string detected file format","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/detect_file_format.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Detect format of results data — detect_file_format","text":"","code":"td2 <- get_test_Tecan_data() detect_file_format(td2$r_files[1]) #> New names: #> • `` -> `...2` #> • `` -> `...3` #> • `` -> `...4` #> • `` -> `...6` #> • `` -> `...7` #> • `` -> `...8` #> • `` -> `...9` #> • `` -> `...10` #> • `` -> `...11` #> [1] \"Tecan\""},{"path":"https://gdrplatform.github.io/gDRimport/reference/dot-check_against_single_template_sheet.html","id":null,"dir":"Reference","previous_headings":"","what":"Evaluate if template file with single sheet is present,\nif the name of the sheet is correct and if it can be fixed — .check_against_single_template_sheet","title":"Evaluate if template file with single sheet is present,\nif the name of the sheet is correct and if it can be fixed — .check_against_single_template_sheet","text":"get sheets given set XLS files","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/dot-check_against_single_template_sheet.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Evaluate if template file with single sheet is present,\nif the name of the sheet is correct and if it can be fixed — .check_against_single_template_sheet","text":"","code":".check_against_single_template_sheet(ts)"},{"path":"https://gdrplatform.github.io/gDRimport/reference/dot-check_against_single_template_sheet.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Evaluate if template file with single sheet is present,\nif the name of the sheet is correct and if it can be fixed — .check_against_single_template_sheet","text":"ts list template sheets info","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/dot-check_against_single_template_sheet.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Evaluate if template file with single sheet is present,\nif the name of the sheet is correct and if it can be fixed — .check_against_single_template_sheet","text":"logical flag","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/dot-check_file_structure.html","id":null,"dir":"Reference","previous_headings":"","what":"Check the structure of raw data — .check_file_structure","title":"Check the structure of raw data — .check_file_structure","text":"Check structure raw data","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/dot-check_file_structure.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check the structure of raw data — .check_file_structure","text":"","code":".check_file_structure(   df,   filename,   sheet_name,   readout_offset,   n_row,   n_col,   bcode_idx,   bcode_col )"},{"path":"https://gdrplatform.github.io/gDRimport/reference/dot-check_file_structure.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check the structure of raw data — .check_file_structure","text":"NULL invisibly.","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/dot-createPseudoData.html","id":null,"dir":"Reference","previous_headings":"","what":"Add in pseudo-data for duration and cell reference division time — .createPseudoData","title":"Add in pseudo-data for duration and cell reference division time — .createPseudoData","text":"Add pseudo-data duration cell reference division time","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/dot-createPseudoData.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add in pseudo-data for duration and cell reference division time — .createPseudoData","text":"","code":".createPseudoData(dt)"},{"path":"https://gdrplatform.github.io/gDRimport/reference/dot-createPseudoData.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add in pseudo-data for duration and cell reference division time — .createPseudoData","text":"data.table","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/dot-extractDoseResponse.html","id":null,"dir":"Reference","previous_headings":"","what":"Get dose and viability readouts and melt into large data table — .extractDoseResponse","title":"Get dose and viability readouts and melt into large data table — .extractDoseResponse","text":"Get dose viability readouts melt large data table","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/dot-extractDoseResponse.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get dose and viability readouts and melt into large data table — .extractDoseResponse","text":"","code":".extractDoseResponse(pset)"},{"path":"https://gdrplatform.github.io/gDRimport/reference/dot-extractDoseResponse.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get dose and viability readouts and melt into large data table — .extractDoseResponse","text":"data.table dose-response data","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/dot-extract_or_create_assay.html","id":null,"dir":"Reference","previous_headings":"","what":"Extracts an assay from a SummarizedExperiment object or creates a new one if it does not exist — .extract_or_create_assay","title":"Extracts an assay from a SummarizedExperiment object or creates a new one if it does not exist — .extract_or_create_assay","text":"function takes SummarizedExperiment object assay name input. specified assay already exists SummarizedExperiment object, returned. Otherwise, new assay specified name created added SummarizedExperiment object. new assay initialized NA values. useful multiple Summarized Experiments given MAE assays. necessary assays Summarized Experiments order convert MAE PSet.","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/dot-extract_or_create_assay.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Extracts an assay from a SummarizedExperiment object or creates a new one if it does not exist — .extract_or_create_assay","text":"","code":".extract_or_create_assay(SE, assay_name)"},{"path":"https://gdrplatform.github.io/gDRimport/reference/dot-extract_or_create_assay.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Extracts an assay from a SummarizedExperiment object or creates a new one if it does not exist — .extract_or_create_assay","text":"SE SummarizedExperiment object assay_name character string specifying name assay extract create","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/dot-extract_or_create_assay.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Extracts an assay from a SummarizedExperiment object or creates a new one if it does not exist — .extract_or_create_assay","text":"SummarizedExperiment object specified assay","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/dot-fill_empty_wells.html","id":null,"dir":"Reference","previous_headings":"","what":"Correct plates with not fully filled readout values — .fill_empty_wells","title":"Correct plates with not fully filled readout values — .fill_empty_wells","text":"Correct plates fully filled readout values","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/dot-fill_empty_wells.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Correct plates with not fully filled readout values — .fill_empty_wells","text":"","code":".fill_empty_wells(   df,   plate_rows,   data_rows,   exp_row,   exp_col,   numeric_regex = \"^\\\\d+$\" )"},{"path":"https://gdrplatform.github.io/gDRimport/reference/dot-fill_empty_wells.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Correct plates with not fully filled readout values — .fill_empty_wells","text":"data.table corrected plates data","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/dot-get_plate_size.html","id":null,"dir":"Reference","previous_headings":"","what":"Get plate size — .get_plate_size","title":"Get plate size — .get_plate_size","text":"Get plate size","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/dot-get_plate_size.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get plate size — .get_plate_size","text":"","code":".get_plate_size(df)"},{"path":"https://gdrplatform.github.io/gDRimport/reference/dot-get_plate_size.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get plate size — .get_plate_size","text":"charvec plate dims","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/dot-get_plate_size.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Get plate size — .get_plate_size","text":"plate sizes assume 1.5x nrows = ncolumns.","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/dot-removeNegatives.html","id":null,"dir":"Reference","previous_headings":"","what":"Remove negative viabilities — .removeNegatives","title":"Remove negative viabilities — .removeNegatives","text":"Remove negative viabilities","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/dot-removeNegatives.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Remove negative viabilities — .removeNegatives","text":"","code":".removeNegatives(dataset)"},{"path":"https://gdrplatform.github.io/gDRimport/reference/dot-removeNegatives.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Remove negative viabilities — .removeNegatives","text":"data.table positive values column ReadoutValue","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/dot-standardize_untreated_values.html","id":null,"dir":"Reference","previous_headings":"","what":"Standardize untreated values to ignore cases — .standardize_untreated_values","title":"Standardize untreated values to ignore cases — .standardize_untreated_values","text":"Standardize untreated values ignore cases","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/dot-standardize_untreated_values.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Standardize untreated values to ignore cases — .standardize_untreated_values","text":"","code":".standardize_untreated_values(df)"},{"path":"https://gdrplatform.github.io/gDRimport/reference/dot-standardize_untreated_values.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Standardize untreated values to ignore cases — .standardize_untreated_values","text":"data.table standardized untreated values","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/enhance_raw_edited_EnVision_df.html","id":null,"dir":"Reference","previous_headings":"","what":"Enhance raw edited EnVision data.table — enhance_raw_edited_EnVision_df","title":"Enhance raw edited EnVision data.table — enhance_raw_edited_EnVision_df","text":"Enhance raw edited EnVision data.table","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/enhance_raw_edited_EnVision_df.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Enhance raw edited EnVision data.table — enhance_raw_edited_EnVision_df","text":"","code":"enhance_raw_edited_EnVision_df(df, barcode_col, headers)"},{"path":"https://gdrplatform.github.io/gDRimport/reference/enhance_raw_edited_EnVision_df.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Enhance raw edited EnVision data.table — enhance_raw_edited_EnVision_df","text":"df raw data.table barcode_col column number barcode data headers list headersa","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/enhance_raw_edited_EnVision_df.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Enhance raw edited EnVision data.table — enhance_raw_edited_EnVision_df","text":"data.table derived EnVision data","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/fix_typos_with_reference.html","id":null,"dir":"Reference","previous_headings":"","what":"Fix typos using reference data — fix_typos_with_reference","title":"Fix typos using reference data — fix_typos_with_reference","text":"Fix typos using reference data Evaluate given list ids try update ","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/fix_typos_with_reference.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fix typos using reference data — fix_typos_with_reference","text":"","code":"fix_typos_with_reference(   data,   ref,   method = c(\"exact\", \"grepl\", \"adist\"),   fix_underscores = FALSE )"},{"path":"https://gdrplatform.github.io/gDRimport/reference/fix_typos_with_reference.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Fix typos using reference data — fix_typos_with_reference","text":"data list charvec(s) charvec data ref charvec reference data method charvec type method used 'exact' used find  identical entries 'ref' data (corrections uppercase'ing) 'grepl' used find entries 'ref' might somehow pre- post- fixed fix_underscores logical flag fix issues underscores data identfiers?","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/fix_typos_with_reference.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Fix typos using reference data — fix_typos_with_reference","text":"list charvec corrected data","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/gDRimport-package.html","id":null,"dir":"Reference","previous_headings":"","what":"gDRimport: Package for handling the import of dose-response data — gDRimport-package","title":"gDRimport: Package for handling the import of dose-response data — gDRimport-package","text":"package part gDR suite. helps prepare raw drug response data downstream processing. mainly contains helper functions importing/loading/validating dose-response data provided different file formats.","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/gDRimport-package.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"gDRimport: Package for handling the import of dose-response data — gDRimport-package","text":"package help page","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/gDRimport-package.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"gDRimport: Package for handling the import of dose-response data — gDRimport-package","text":"learn functions start help(package = \"gDRimport\")","code":""},{"path":[]},{"path":"https://gdrplatform.github.io/gDRimport/reference/gDRimport-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"gDRimport: Package for handling the import of dose-response data — gDRimport-package","text":"Maintainer: Arkadiusz Gladki gladki.arkadiusz@gmail.com (ORCID) Authors: Bartosz Czech (ORCID) Marc Hafner (ORCID) Sergiu Mocanu Dariusz Scigocki Allison Vuong Luca Gerosa (ORCID) Janina Smola","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/gdr_test_data-class.html","id":null,"dir":"Reference","previous_headings":"","what":"gDR Test Data object — gdr_test_data-class","title":"gDR Test Data object — gdr_test_data-class","text":"Object class gdr_test_data build function get_test_data()","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/gdr_test_data-class.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"gDR Test Data object — gdr_test_data-class","text":"object class gdr_test_data primary test data","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/gdr_test_data-class.html","id":"slots","dir":"Reference","previous_headings":"","what":"Slots","title":"gDR Test Data object — gdr_test_data-class","text":"manifest_path character, path manifest file result_path character, path(s) results file template_path character, path(s) data.table template data ref_m_df character, data.table manifest data ref_r1_r2 character, path reference file raw data treated & untreated ref_r1 character, path reference file raw data treated ref_t1_t2 character, path reference template file treated & untreated data ref_t1 character, path reference template file treated data","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/getPSet.html","id":null,"dir":"Reference","previous_headings":"","what":"Get PharmacoSet — getPSet","title":"Get PharmacoSet — getPSet","text":"Get PharmacoSet","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/getPSet.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get PharmacoSet — getPSet","text":"","code":"getPSet(   pset_name,   psetDir = getwd(),   canonical = FALSE,   timeout = 600,   use_local_PSets_list = FALSE )"},{"path":"https://gdrplatform.github.io/gDRimport/reference/getPSet.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get PharmacoSet — getPSet","text":"pset_name string name PharmacoSet psetDir string temporary directory PharmacoSet canonical logical flag indicating PSet canonical timeout maximum number seconds allowed PSet download use_local_PSets_list logical flag PSets list used local. FALSE PSets list taken web.","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/getPSet.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get PharmacoSet — getPSet","text":"PharmacoSet object","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/getPSet.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get PharmacoSet — getPSet","text":"","code":"suppressMessages(getPSet(   \"Tavor_2020\",    psetDir = system.file(\"extdata/pset\", package = \"gDRimport\"),   use_local_PSets_list = TRUE )) #> <PharmacoSet> #> Name:  Tavor  #> Date Created:  Fri Feb  4 17:32:17 2022  #> Number of samples:  53  #> Molecular profiles: #> RNAseq : #>   Dim: 24137, 43  #> Treatment response: #> Drug pertubation: #>    Please look at pertNumber(cSet) to determine number of experiments  for each drug-sample combination. #> Drug sensitivity: #>    Number of Experiments:  2668  #>    Please look at sensNumber(cSet) to determine number of  experiments for each drug-sample combination."},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_EnVision_properties.html","id":null,"dir":"Reference","previous_headings":"","what":"Get properties of EnVision data — get_EnVision_properties","title":"Get properties of EnVision data — get_EnVision_properties","text":"function return properties EnVision data","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_EnVision_properties.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get properties of EnVision data — get_EnVision_properties","text":"","code":"get_EnVision_properties(results.list, fname)"},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_EnVision_properties.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get properties of EnVision data — get_EnVision_properties","text":"results.list list EnVision data fname name input file","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_EnVision_properties.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get properties of EnVision data — get_EnVision_properties","text":"list EnVision propertiesa","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_df_from_raw_edited_EnVision_df.html","id":null,"dir":"Reference","previous_headings":"","what":"Get final results (as a data.table)\nfrom raw edited EnVision data.table — get_df_from_raw_edited_EnVision_df","title":"Get final results (as a data.table)\nfrom raw edited EnVision data.table — get_df_from_raw_edited_EnVision_df","text":"Get final results (data.table) raw edited EnVision data.table","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_df_from_raw_edited_EnVision_df.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get final results (as a data.table)\nfrom raw edited EnVision data.table — get_df_from_raw_edited_EnVision_df","text":"","code":"get_df_from_raw_edited_EnVision_df(   df,   barcode_idx,   barcode_col,   n_row,   n_col,   fname,   sheet_name,   headers )"},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_df_from_raw_edited_EnVision_df.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get final results (as a data.table)\nfrom raw edited EnVision data.table — get_df_from_raw_edited_EnVision_df","text":"df raw data.table barcode_idx numeric vector barcode indices barcode_col column number barcode data n_row number rows n_col number columns fname file name sheet_name name Excel sheet headers list headersa","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_df_from_raw_edited_EnVision_df.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get final results (as a data.table)\nfrom raw edited EnVision data.table — get_df_from_raw_edited_EnVision_df","text":"data.table derived EnVision data","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_df_from_raw_unedited_EnVision_df.html","id":null,"dir":"Reference","previous_headings":"","what":"Get final results (as a data.table)\nfrom raw unedited EnVision data.table — get_df_from_raw_unedited_EnVision_df","title":"Get final results (as a data.table)\nfrom raw unedited EnVision data.table — get_df_from_raw_unedited_EnVision_df","text":"Get final results (data.table) raw unedited EnVision data.table","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_df_from_raw_unedited_EnVision_df.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get final results (as a data.table)\nfrom raw unedited EnVision data.table — get_df_from_raw_unedited_EnVision_df","text":"","code":"get_df_from_raw_unedited_EnVision_df(df, n_row, n_col, barcode_col)"},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_df_from_raw_unedited_EnVision_df.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get final results (as a data.table)\nfrom raw unedited EnVision data.table — get_df_from_raw_unedited_EnVision_df","text":"df raw data.table n_row number rows n_col number columns barcode_col column number barcode data","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_df_from_raw_unedited_EnVision_df.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get final results (as a data.table)\nfrom raw unedited EnVision data.table — get_df_from_raw_unedited_EnVision_df","text":"data.table derived EnVision data","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_excel_sheet_names.html","id":null,"dir":"Reference","previous_headings":"","what":"get Excel sheets names for a charvec of files\nfor non-Excel files return 0 — get_excel_sheet_names","title":"get Excel sheets names for a charvec of files\nfor non-Excel files return 0 — get_excel_sheet_names","text":"get Excel sheets names charvec files non-Excel files return 0","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_excel_sheet_names.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"get Excel sheets names for a charvec of files\nfor non-Excel files return 0 — get_excel_sheet_names","text":"","code":"get_excel_sheet_names(fls)"},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_excel_sheet_names.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"get Excel sheets names for a charvec of files\nfor non-Excel files return 0 — get_excel_sheet_names","text":"fls charvec file pathsa","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_excel_sheet_names.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"get Excel sheets names for a charvec of files\nfor non-Excel files return 0 — get_excel_sheet_names","text":"list one element per file sheet names 0 (non-Excel file)","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_exception_data.html","id":null,"dir":"Reference","previous_headings":"","what":"get exception data — get_exception_data","title":"get exception data — get_exception_data","text":"get exception data","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_exception_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"get exception data — get_exception_data","text":"","code":"get_exception_data(status_code = NULL)"},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_exception_data.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"get exception data — get_exception_data","text":"status_code numeric value","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_exception_data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"get exception data — get_exception_data","text":"data.table row exception data exceptions","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_exception_data.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"get exception data — get_exception_data","text":"","code":"get_exception_data(1) #>    status_code                  title #>         <char>                 <char> #> 1:           1 Error loading manifest #>                                         sprintf_text   type input_type #>                                               <char> <char>     <char> #> 1: There were errors loading manifest. See logs:\\n%s  error   manifest get_exception_data() #>     status_code                                    title #>          <char>                                   <char> #>  1:           1                   Error loading manifest #>  2:           2                       Manifest not found #>  3:           3                  Error loading treatment #>  4:           4                Warning loading treatment #>  5:           5                  Error loading treatment #>  6:           6     Missing data for some Barcode, Plate #>  7:           7     Missing data for some Barcode, Plate #>  8:           8                   Error loading raw data #>  9:           9                   Error loading raw data #> 10:          10                Error during merging data #> 11:          11                  Missing treatment files #> 12:          12                   Error reading Manifest #> 13:          13                     Manifest file format #> 14:          14                        Manifest barcodes #> 15:          15                       Treatment controls #> 16:          16                          Instrument type #> 17:          17                     Treatment sheet name #> 18:          18                     Treatment entry name #> 19:          19                  Error loading treatment #> 20:          20         Error loading specific treatment #> 21:          21          Error reading specific raw data #> 22:          22 Error reading sheet in the raw data file #> 23:          23      Error with readout values in plates #> 24:          24             Error with treatment headers #> 25:          25         Error with treatment file sheets #> 26:          26              Metadata special characters #> 27:          27                         Metadata invalid #> 28:          28                       Raw Data delimiter #> 29:          29                        Raw Data EnVision #> 30:          30                      Raw Data Plate size #> 31:          31                       Raw Data structure #> 32:          32 Treatment File Gnumber and Concentration #> 33:          33                Error loading input files #> 34:          34                  Missing drug annotation #> 35:          35             Missing cell line annotation #> 36:          36                    Invalid averaged data #>     status_code                                    title #>                                                                                                                                                                                                      sprintf_text #>                                                                                                                                                                                                            <char> #>  1:                                                                                                                                                             There were errors loading manifest. See logs:\\n%s #>  2:                                                                                                                                                                                         Please load manifest! #>  3:                                                         Some of the treatment files entered in the manifest have not been uploaded:\\n%s\\nPlease check the uploaded files and their name (including extension) #>  4:                                                                                                                                                                     Some uploaded files (**%s**) are not used #>  5:                                                                                                                                                  There were errors when loading the treatments. See logs:\\n%s #>  6:                                                                                                           Some plates (**%s**) found in the manifest are not reported in the data files and will be discarded #>  7:                                                                                                           Some plates (**%s**) found in the data files are not reported in the manifest and will be discarded #>  8:                                                                                                                         Txt file in an unsupported format. Please check if the file uses tab(\\t) as separator #>  9:                                                                                                                                                        There were errors when loading raw data. See logs:\\n%s #> 10:                                                                                                                                                            There were errors when merging data. See logs:\\n%s #> 11:                                                                                                                                                                          Some treatment files are missing: %s #> 12:                                                                                                                                         There were errors reading the manifest file. Please see the logs:\\n%s #> 13:                                                                                                                         %s file format is not supported. Please convert your file to one of the following: %s #> 14:                                                                                                                                                                          Barcodes in Manifest must be unique! #> 15:                                                                                                                   No untreated controls were found in the treatment. Please upload the appropriate treatment. #> 16:                                                                                                                                                                                  Unrecognized instrument type #> 17:                                                                                                                                                         In untreated treatment file %s, sheet name must be %s #> 18:                                                                                                                                                            In untreated treatment file %s, entries must be %s #> 19:                                                                                                                                             There were errors loading the treatment. Please see the logs:\\n%s #> 20:                                                                                                                                                 There were errors loading treatment %s. Please see logs: \\n%s #> 21:                                                                                                                                                                                              Error reading %s #> 22:                                                                                                                                                                                    Error reading %s, sheet %s #> 23:                                                                                                                                        In result file %s (sheet %s) readout values are misplaced for plate %s #> 24:                                                                    Treatment does not contain all expected headers for a '%s'. '%s' is/are required. Please correct your treatment or change the identifiers. #> 25:                                                                                                                                  Treatment file %s does not contain %s sheets. Please correct your treatment. #> 26:                                                                                                                      Metadata field names for %s cannot contain special characters or start with a number: %s #> 27:                                                                                                                                              Metadata field name: %s in %s is not valid (reserved for output) #> 28:                                                                                                                                                             Can't guess separator for the delimited files: %s #> 29:                                                                                                                                                          Error reading %s: not an original EnVision .csv file #> 30:                                                                                                                                                                            Error reading %s: wrong plate size #> 31:                                                                                                                                       In result file %s (sheet %s) readout values are misplaced for plate %s. #> 32:                           Treatment file(s) %s do/does not contain the same number of Gnumber_* and Concentration_* sheets. Gnumber_* and Concentration_* sheets are required. Please correct your treatment. #> 33:                                                                                         Some input files are missing. Please upload only files with names starting with Manifest_*, Treatment_* and RawData_* #> 34:                                                                                                                 The following drugs IDs are missing: '%s'. <br>Don't worry, drug names will be used for them. #> 35:                                                                                                        The following cell line IDs are missing: '%s'. <br>Don't worry, cell line names will be used for them. #> 36: Averaged dose-response data for the selected cell line and drug: '%s' can be considered invalid. Please check your data in the module 'Manage Data' or contact gdrplatform team via 'gdr-support-d@gene.com'. #>                                                                                                                                                                                                      sprintf_text #>        type   input_type #>      <char>       <char> #>  1:   error     manifest #>  2:   error     manifest #>  3:   error    treatment #>  4: warning    treatment #>  5:   error    treatment #>  6: warning     manifest #>  7: warning     manifest #>  8:   error     raw data #>  9:   error     raw data #> 10:   error merging data #> 11:   error    treatment #> 12:   error     manifest #> 13:   error     manifest #> 14:   error     manifest #> 15:   error    treatment #> 16:   error     raw data #> 17:   error    treatment #> 18:   error    treatment #> 19:   error    treatment #> 20:   error    treatment #> 21:   error     raw data #> 22:   error     raw data #> 23:   error     raw data #> 24:   error    treatment #> 25:   error    treatment #> 26:   error     metadata #> 27:   error     metadata #> 28:   error     raw data #> 29:   error     raw data #> 30:   error     raw data #> 31:   error     raw data #> 32:   error    treatment #> 33:   error  input files #> 34: warning   submit tab #> 35: warning   submit tab #> 36:   error   assay data #>        type   input_type"},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_expected_template_sheets.html","id":null,"dir":"Reference","previous_headings":"","what":"Get names of the sheets expected in templates xlsx — get_expected_template_sheets","title":"Get names of the sheets expected in templates xlsx — get_expected_template_sheets","text":"Get names sheets expected templates xlsx","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_expected_template_sheets.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get names of the sheets expected in templates xlsx — get_expected_template_sheets","text":"","code":"get_expected_template_sheets(type = c(\"all\", \"core\", \"optional\"))"},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_expected_template_sheets.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get names of the sheets expected in templates xlsx — get_expected_template_sheets","text":"type charvec type sheets","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_expected_template_sheets.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get names of the sheets expected in templates xlsx — get_expected_template_sheets","text":"string type sheets","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_plate_info_from_template_xlsx.html","id":null,"dir":"Reference","previous_headings":"","what":"Get plate info from template xlsx — get_plate_info_from_template_xlsx","title":"Get plate info from template xlsx — get_plate_info_from_template_xlsx","text":"Get plate info template xlsx","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_plate_info_from_template_xlsx.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get plate info from template xlsx — get_plate_info_from_template_xlsx","text":"","code":"get_plate_info_from_template_xlsx(template_file, Gnumber_idx, idx)"},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_plate_info_from_template_xlsx.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get plate info from template xlsx — get_plate_info_from_template_xlsx","text":"template_file character, file path(s) template(s) Gnumber_idx index Gnumber data idx template file index","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_plate_info_from_template_xlsx.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get plate info from template xlsx — get_plate_info_from_template_xlsx","text":"list plate info","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_test_D300_data.html","id":null,"dir":"Reference","previous_headings":"","what":"get test D300 data — get_test_D300_data","title":"get test D300 data — get_test_D300_data","text":"get test D300 data","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_test_D300_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"get test D300 data — get_test_D300_data","text":"","code":"get_test_D300_data()"},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_test_D300_data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"get test D300 data — get_test_D300_data","text":"list input data (manifest/template/result paths) related reference data (qs file paths)","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_test_D300_data.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"get test D300 data — get_test_D300_data","text":"","code":"get_test_D300_data() #> $f_96w #> $f_96w$d300 #> [1] \"/usr/local/lib/R/site-library/gDRimport/extdata/data3/D300_96_well_plate_example.tdd\" #>  #> $f_96w$Gnum #> [1] \"/usr/local/lib/R/site-library/gDRimport/extdata/data3/Gnumber_D300_96_well_plate.xlsx\" #>  #> $f_96w$dest_path #> [1] \"/usr/local/lib/R/site-library/gDRimport/extdata/data3/output_files_96w/output\" #>  #> $f_96w$ref_d300 #> [1] \"/usr/local/lib/R/site-library/gDRimport/extdata/data3/ref_D300_96_well_plate_example.qs\" #>  #> $f_96w$ref_Gnum #> [1] \"/usr/local/lib/R/site-library/gDRimport/extdata/data3/ref_Gnumber_D300_96_well_plate.qs\" #>  #> $f_96w$ref_output_path #> [1] \"/usr/local/lib/R/site-library/gDRimport/extdata/data3/output_files_96w/reference\" #>  #>  #> $f_384w #> $f_384w$d300 #> [1] \"/usr/local/lib/R/site-library/gDRimport/extdata/data3/D300_384_well_plate_example.tdd\" #>  #> $f_384w$Gnum #> [1] \"/usr/local/lib/R/site-library/gDRimport/extdata/data3/Gnumber_D300_384_well_plate.xlsx\" #>  #> $f_384w$ref_Gnum #> [1] \"/usr/local/lib/R/site-library/gDRimport/extdata/data3/ref_Gnumber_D300_384_well_plate.qs\" #>  #> $f_384w$ref_d300 #> [1] \"/usr/local/lib/R/site-library/gDRimport/extdata/data3/ref_D300_384_well_plate_example.qs\" #>  #> $f_384w$dest_path #> [1] \"/usr/local/lib/R/site-library/gDRimport/extdata/data3/output_files_384w/output\" #>  #> $f_384w$ref_output_path #> [1] \"/usr/local/lib/R/site-library/gDRimport/extdata/data3/output_files_384w/reference\" #>  #>"},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_test_EnVision_data.html","id":null,"dir":"Reference","previous_headings":"","what":"get test EnVision data — get_test_EnVision_data","title":"get test EnVision data — get_test_EnVision_data","text":"get test EnVision data","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_test_EnVision_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"get test EnVision data — get_test_EnVision_data","text":"","code":"get_test_EnVision_data()"},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_test_EnVision_data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"get test EnVision data — get_test_EnVision_data","text":"list input data (manifest/template/result paths) related reference data (.qs file paths)","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_test_EnVision_data.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"get test EnVision data — get_test_EnVision_data","text":"","code":"get_test_EnVision_data() #> $m_file #> [1] \"/usr/local/lib/R/site-library/gDRimport/extdata/data4/Manifest.xlsx\" #>  #> $r_files #>  [1] \"/usr/local/lib/R/site-library/gDRimport/extdata/data4/H0109269D00.csv\" #>  [2] \"/usr/local/lib/R/site-library/gDRimport/extdata/data4/H0109269D01.csv\" #>  [3] \"/usr/local/lib/R/site-library/gDRimport/extdata/data4/H0309269D00.csv\" #>  [4] \"/usr/local/lib/R/site-library/gDRimport/extdata/data4/H0309269D01.csv\" #>  [5] \"/usr/local/lib/R/site-library/gDRimport/extdata/data4/H0409269D00.csv\" #>  [6] \"/usr/local/lib/R/site-library/gDRimport/extdata/data4/H0409269D01.csv\" #>  [7] \"/usr/local/lib/R/site-library/gDRimport/extdata/data4/H0509269D00.csv\" #>  [8] \"/usr/local/lib/R/site-library/gDRimport/extdata/data4/H0509269D01.csv\" #>  [9] \"/usr/local/lib/R/site-library/gDRimport/extdata/data4/H0609269D00.csv\" #> [10] \"/usr/local/lib/R/site-library/gDRimport/extdata/data4/H0609269D01.csv\" #> [11] \"/usr/local/lib/R/site-library/gDRimport/extdata/data4/H0709269D00.csv\" #> [12] \"/usr/local/lib/R/site-library/gDRimport/extdata/data4/H0709269D01.csv\" #> [13] \"/usr/local/lib/R/site-library/gDRimport/extdata/data4/H0809269D00.csv\" #> [14] \"/usr/local/lib/R/site-library/gDRimport/extdata/data4/H0809269D01.csv\" #> [15] \"/usr/local/lib/R/site-library/gDRimport/extdata/data4/H0909269D00.csv\" #> [16] \"/usr/local/lib/R/site-library/gDRimport/extdata/data4/H0909269D01.csv\" #> [17] \"/usr/local/lib/R/site-library/gDRimport/extdata/data4/H1109269D00.csv\" #> [18] \"/usr/local/lib/R/site-library/gDRimport/extdata/data4/H1109269D01.csv\" #> [19] \"/usr/local/lib/R/site-library/gDRimport/extdata/data4/H1209269D00.csv\" #> [20] \"/usr/local/lib/R/site-library/gDRimport/extdata/data4/H1209269D01.csv\" #> [21] \"/usr/local/lib/R/site-library/gDRimport/extdata/data4/H1409269D00.csv\" #> [22] \"/usr/local/lib/R/site-library/gDRimport/extdata/data4/H1409269D01.csv\" #> [23] \"/usr/local/lib/R/site-library/gDRimport/extdata/data4/K0209269D00.csv\" #> [24] \"/usr/local/lib/R/site-library/gDRimport/extdata/data4/K0209269D01.csv\" #> [25] \"/usr/local/lib/R/site-library/gDRimport/extdata/data4/K0809269D00.csv\" #> [26] \"/usr/local/lib/R/site-library/gDRimport/extdata/data4/K0809269D01.csv\" #> [27] \"/usr/local/lib/R/site-library/gDRimport/extdata/data4/K1009269D00.csv\" #> [28] \"/usr/local/lib/R/site-library/gDRimport/extdata/data4/K1009269D01.csv\" #>  #> $t_files #> [1] \"/usr/local/lib/R/site-library/gDRimport/extdata/data4/Project40.treated.template.xlsx\"   #> [2] \"/usr/local/lib/R/site-library/gDRimport/extdata/data4/Project40.untreated.template.xlsx\" #>  #> $ref_l_path #> [1] \"/usr/local/lib/R/site-library/gDRimport/extdata/data4/ref_l.qs\" #>"},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_test_Tecan_data.html","id":null,"dir":"Reference","previous_headings":"","what":"get test Tecan data — get_test_Tecan_data","title":"get test Tecan data — get_test_Tecan_data","text":"get test Tecan data","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_test_Tecan_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"get test Tecan data — get_test_Tecan_data","text":"","code":"get_test_Tecan_data()"},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_test_Tecan_data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"get test Tecan data — get_test_Tecan_data","text":"list input data (manifest/template/result paths) related reference data (qs file paths)","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_test_Tecan_data.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"get test Tecan data — get_test_Tecan_data","text":"","code":"get_test_Tecan_data() #> $m_file #> [1] \"/usr/local/lib/R/site-library/gDRimport/extdata/data2/manifest_Tecan_96_well_plates.xlsx\" #>  #> $r_files #> [1] \"/usr/local/lib/R/site-library/gDRimport/extdata/data2/RawData_Tecan_96_well_plates.xlsx\" #>  #> $t_files #> [1] \"/usr/local/lib/R/site-library/gDRimport/extdata/data2/D300_trt_Tecan_96_well_plates.xlsx\" #>  #> $ref_m_df #> [1] \"/usr/local/lib/R/site-library/gDRimport/extdata/data2/ref_manifest_Tecan_96_well_plates.qs\" #>  #> $ref_r_df #> [1] \"/usr/local/lib/R/site-library/gDRimport/extdata/data2/ref_RawData_Tecan_96_well_plates.qs\" #>  #> $ref_t_df #> [1] \"/usr/local/lib/R/site-library/gDRimport/extdata/data2/ref_D300_trt_Tecan_96_well_plates.qs\" #>"},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_test_data.html","id":null,"dir":"Reference","previous_headings":"","what":"get primary test data — get_test_data","title":"get primary test data — get_test_data","text":"get primary test data","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_test_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"get primary test data — get_test_data","text":"","code":"get_test_data()"},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_test_data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"get primary test data — get_test_data","text":"object class \"gdr_test_data\" input data (manifest/template/result paths) related reference data (qs file paths)","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_test_data.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"get primary test data — get_test_data","text":"","code":"get_test_data() #> class: gdr_test_data  #> slots: manifest_path result_path template_path ref_m_df ref_r1_r2 ref_r1 ref_t1_t2 ref_t1"},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_test_tsv_data.html","id":null,"dir":"Reference","previous_headings":"","what":"get test tsv data — get_test_tsv_data","title":"get test tsv data — get_test_tsv_data","text":"get test tsv data","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_test_tsv_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"get test tsv data — get_test_tsv_data","text":"","code":"get_test_tsv_data()"},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_test_tsv_data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"get test tsv data — get_test_tsv_data","text":"list input data (manifest/template/result paths) related reference data (.qs file paths)","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_test_tsv_data.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"get test tsv data — get_test_tsv_data","text":"","code":"get_test_tsv_data() #> $m_file #> [1] \"/usr/local/lib/R/site-library/gDRimport/extdata/data5/Manifest.tsv\" #>  #> $r_files #> [1] \"/usr/local/lib/R/site-library/gDRimport/extdata/data5/RawData.tsv\" #>  #> $t_files #> [1] \"/usr/local/lib/R/site-library/gDRimport/extdata/data5/Template_trt.tsv\"   #> [2] \"/usr/local/lib/R/site-library/gDRimport/extdata/data5/Template_untrt.tsv\" #>  #> $ref_l_path #> [1] \"/usr/local/lib/R/site-library/gDRimport/extdata/data5/ref_l.qs\" #>"},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_xl_sheets.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Excel sheets — get_xl_sheets","title":"Get Excel sheets — get_xl_sheets","text":"get sheets given set XLS files","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_xl_sheets.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Excel sheets — get_xl_sheets","text":"","code":"get_xl_sheets(files)"},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_xl_sheets.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Excel sheets — get_xl_sheets","text":"files charvec file paths","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/get_xl_sheets.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Excel sheets — get_xl_sheets","text":"named list names excel filenames values sheets within file","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/import_D300.html","id":null,"dir":"Reference","previous_headings":"","what":"Import D300 — import_D300","title":"Import D300 — import_D300","text":"functions takes D300 file generates corresponding template files","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/import_D300.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Import D300 — import_D300","text":"","code":"import_D300(D300_file, metadata_file, destination_path)"},{"path":"https://gdrplatform.github.io/gDRimport/reference/import_D300.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Import D300 — import_D300","text":"D300_file character, file path D300 file metadata_file character, file path file mapping D300 names Gnumbers destination_path character, path folder template files generated","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/import_D300.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Import D300 — import_D300","text":"Create one Excel file per plate. sheet plate file describes drugs corrresponding concentrations tested well.","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/import_D300.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Import D300 — import_D300","text":"example, wells treated 2 drugs combination result 4 sheets per plate. Sheet 1: Drug 1 Sheet 2: Conc Drug 1 Sheet 3: Drug 2 Sheet 4: Conc Drug 2","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/import_D300.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Import D300 — import_D300","text":"","code":"td3 <- get_test_D300_data()[[\"f_96w\"]] o_path <- file.path(tempdir(), \"td3\") dir.create(o_path) import_D300(td3$d300, td3$Gnum, o_path) list.files(o_path) #>  [1] \"trt_P1.xlsx\"  \"trt_P10.xlsx\" \"trt_P11.xlsx\" \"trt_P12.xlsx\" \"trt_P13.xlsx\" #>  [6] \"trt_P14.xlsx\" \"trt_P15.xlsx\" \"trt_P16.xlsx\" \"trt_P17.xlsx\" \"trt_P18.xlsx\" #> [11] \"trt_P19.xlsx\" \"trt_P2.xlsx\"  \"trt_P20.xlsx\" \"trt_P21.xlsx\" \"trt_P22.xlsx\" #> [16] \"trt_P3.xlsx\"  \"trt_P4.xlsx\"  \"trt_P5.xlsx\"  \"trt_P6.xlsx\"  \"trt_P7.xlsx\"  #> [21] \"trt_P8.xlsx\"  \"trt_P9.xlsx\"  unlink(o_path, recursive = TRUE)"},{"path":"https://gdrplatform.github.io/gDRimport/reference/is_readable_v.html","id":null,"dir":"Reference","previous_headings":"","what":"is_readable_v\nCheck if all paths in vector are readable — is_readable_v","title":"is_readable_v\nCheck if all paths in vector are readable — is_readable_v","text":"is_readable_v Check paths vector readable","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/is_readable_v.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"is_readable_v\nCheck if all paths in vector are readable — is_readable_v","text":"","code":"is_readable_v(paths)"},{"path":"https://gdrplatform.github.io/gDRimport/reference/is_readable_v.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"is_readable_v\nCheck if all paths in vector are readable — is_readable_v","text":"paths character path(s)","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/is_readable_v.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"is_readable_v\nCheck if all paths in vector are readable — is_readable_v","text":"NULL invisibly.","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/is_readable_v.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"is_readable_v\nCheck if all paths in vector are readable — is_readable_v","text":"","code":"td2 <- get_test_Tecan_data() is_readable_v(td2$r_files) #> [1] TRUE"},{"path":"https://gdrplatform.github.io/gDRimport/reference/load_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Load data — load_data","title":"Load data — load_data","text":"functions loads checks data file(s)","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/load_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Load data — load_data","text":"","code":"load_data(   manifest_file,   df_template_files,   results_file,   instrument = \"EnVision\" )"},{"path":"https://gdrplatform.github.io/gDRimport/reference/load_data.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Load data — load_data","text":"manifest_file character, file path(s) manifest(s) df_template_files data.table, datapaths names results file(s) character file path templates file(s) results_file data.table, datapaths names results file(s) character file path results file(s) instrument character","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/load_data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Load data — load_data","text":"list three data.tables manifest/treatment results","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/load_data.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Load data — load_data","text":"","code":"td <- get_test_data()  l_tbl <- load_data(manifest_path(td), template_path(td), result_path(td)) #> INFO [2024-12-09 10:53:16] Manifest loaded successfully #> INFO [2024-12-09 10:53:16] Reading Template_7daytreated.xlsx with load_templates_xlsx #> INFO [2024-12-09 10:53:16] Loading Template_7daytreated.xlsx #> INFO [2024-12-09 10:53:17] Loading Template_Untreated.xlsx #> INFO [2024-12-09 10:53:17] Templates loaded successfully! #> INFO [2024-12-09 10:53:17] Reading file /usr/local/lib/R/site-library/gDRimport/extdata/data1/RawData_day0.xlsx, sheet Readout_0077vs0068_day7 #> New names: #> • `` -> `...1` #> • `` -> `...2` #> • `` -> `...3` #> • `` -> `...4` #> • `` -> `...5` #> • `` -> `...6` #> • `` -> `...7` #> • `` -> `...8` #> • `` -> `...9` #> • `` -> `...10` #> • `` -> `...11` #> • `` -> `...12` #> • `` -> `...13` #> • `` -> `...14` #> • `` -> `...15` #> • `` -> `...16` #> • `` -> `...17` #> • `` -> `...18` #> • `` -> `...19` #> • `` -> `...20` #> • `` -> `...21` #> • `` -> `...22` #> • `` -> `...23` #> • `` -> `...24` #> • `` -> `...25` #> INFO [2024-12-09 10:53:17] Plate 201904190a read; 384 wells #> INFO [2024-12-09 10:53:17] Plate 201904190b read; 384 wells #> INFO [2024-12-09 10:53:17] Plate 201904190c read; 384 wells #> INFO [2024-12-09 10:53:17] Plate 201904190d read; 384 wells #> INFO [2024-12-09 10:53:17] Plate 201904190e read; 384 wells #> INFO [2024-12-09 10:53:17] Plate 201904190f read; 384 wells #> INFO [2024-12-09 10:53:17] File done #> INFO [2024-12-09 10:53:17] Reading file /usr/local/lib/R/site-library/gDRimport/extdata/data1/RawData_day7.xlsx, sheet Readout_0077vs0068_day7 #> New names: #> • `` -> `...1` #> • `` -> `...2` #> • `` -> `...3` #> • `` -> `...4` #> • `` -> `...5` #> • `` -> `...6` #> • `` -> `...7` #> • `` -> `...8` #> • `` -> `...9` #> • `` -> `...10` #> • `` -> `...11` #> • `` -> `...12` #> • `` -> `...13` #> • `` -> `...14` #> • `` -> `...15` #> • `` -> `...16` #> • `` -> `...17` #> • `` -> `...18` #> • `` -> `...19` #> • `` -> `...20` #> • `` -> `...21` #> • `` -> `...22` #> • `` -> `...23` #> • `` -> `...24` #> • `` -> `...25` #> INFO [2024-12-09 10:53:17] Plate 201904197a read; 384 wells #> INFO [2024-12-09 10:53:17] Plate 201904197b read; 384 wells #> INFO [2024-12-09 10:53:17] Plate 201904197c read; 384 wells #> INFO [2024-12-09 10:53:17] Plate 201904197d read; 384 wells #> INFO [2024-12-09 10:53:17] Plate 201904197e read; 384 wells #> INFO [2024-12-09 10:53:17] Plate 201904197f read; 384 wells #> INFO [2024-12-09 10:53:17] File done"},{"path":"https://gdrplatform.github.io/gDRimport/reference/load_manifest.html","id":null,"dir":"Reference","previous_headings":"","what":"Load manifest — load_manifest","title":"Load manifest — load_manifest","text":"functions loads checks manifest file(s)","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/load_manifest.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Load manifest — load_manifest","text":"","code":"load_manifest(manifest_file)"},{"path":"https://gdrplatform.github.io/gDRimport/reference/load_manifest.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Load manifest — load_manifest","text":"manifest_file character, file path(s) manifest(s)","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/load_manifest.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Load manifest — load_manifest","text":"list manifest data.table headers","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/load_manifest.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Load manifest — load_manifest","text":"","code":"td <- get_test_data()  ml <- load_manifest(manifest_path(td)) #> INFO [2024-12-09 10:53:17] Manifest loaded successfully"},{"path":"https://gdrplatform.github.io/gDRimport/reference/load_results.html","id":null,"dir":"Reference","previous_headings":"","what":"Load results — load_results","title":"Load results — load_results","text":"functions loads checks results file(s)","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/load_results.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Load results — load_results","text":"","code":"load_results(   df_results_files,   instrument = \"EnVision\",   headers = gDRutils::get_env_identifiers() )"},{"path":"https://gdrplatform.github.io/gDRimport/reference/load_results.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Load results — load_results","text":"df_results_files data.table, datapaths names results file(s) character file path results file(s) instrument character headers list headers identified manifest file","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/load_results.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Load results — load_results","text":"data.table results' data","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/load_results.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Load results — load_results","text":"","code":"td <- get_test_data()  r_df <- load_results(result_path(td)) #> INFO [2024-12-09 10:53:17] Reading file /usr/local/lib/R/site-library/gDRimport/extdata/data1/RawData_day0.xlsx, sheet Readout_0077vs0068_day7 #> New names: #> • `` -> `...1` #> • `` -> `...2` #> • `` -> `...3` #> • `` -> `...4` #> • `` -> `...5` #> • `` -> `...6` #> • `` -> `...7` #> • `` -> `...8` #> • `` -> `...9` #> • `` -> `...10` #> • `` -> `...11` #> • `` -> `...12` #> • `` -> `...13` #> • `` -> `...14` #> • `` -> `...15` #> • `` -> `...16` #> • `` -> `...17` #> • `` -> `...18` #> • `` -> `...19` #> • `` -> `...20` #> • `` -> `...21` #> • `` -> `...22` #> • `` -> `...23` #> • `` -> `...24` #> • `` -> `...25` #> INFO [2024-12-09 10:53:18] Plate 1 read; 384 wells #> INFO [2024-12-09 10:53:18] Plate 2 read; 384 wells #> INFO [2024-12-09 10:53:18] Plate 3 read; 384 wells #> INFO [2024-12-09 10:53:18] Plate 4 read; 384 wells #> INFO [2024-12-09 10:53:18] Plate 5 read; 384 wells #> INFO [2024-12-09 10:53:18] Plate 6 read; 384 wells #> INFO [2024-12-09 10:53:18] File done #> INFO [2024-12-09 10:53:18] Reading file /usr/local/lib/R/site-library/gDRimport/extdata/data1/RawData_day7.xlsx, sheet Readout_0077vs0068_day7 #> New names: #> • `` -> `...1` #> • `` -> `...2` #> • `` -> `...3` #> • `` -> `...4` #> • `` -> `...5` #> • `` -> `...6` #> • `` -> `...7` #> • `` -> `...8` #> • `` -> `...9` #> • `` -> `...10` #> • `` -> `...11` #> • `` -> `...12` #> • `` -> `...13` #> • `` -> `...14` #> • `` -> `...15` #> • `` -> `...16` #> • `` -> `...17` #> • `` -> `...18` #> • `` -> `...19` #> • `` -> `...20` #> • `` -> `...21` #> • `` -> `...22` #> • `` -> `...23` #> • `` -> `...24` #> • `` -> `...25` #> INFO [2024-12-09 10:53:18] Plate 1 read; 384 wells #> INFO [2024-12-09 10:53:18] Plate 2 read; 384 wells #> INFO [2024-12-09 10:53:18] Plate 3 read; 384 wells #> INFO [2024-12-09 10:53:18] Plate 4 read; 384 wells #> INFO [2024-12-09 10:53:18] Plate 5 read; 384 wells #> INFO [2024-12-09 10:53:18] Plate 6 read; 384 wells #> INFO [2024-12-09 10:53:18] File done"},{"path":"https://gdrplatform.github.io/gDRimport/reference/load_results_EnVision.html","id":null,"dir":"Reference","previous_headings":"","what":"Load EnVision results from xlsx — load_results_EnVision","title":"Load EnVision results from xlsx — load_results_EnVision","text":"functions loads checks results file(s)","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/load_results_EnVision.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Load EnVision results from xlsx — load_results_EnVision","text":"","code":"load_results_EnVision(results_file, headers = gDRutils::get_env_identifiers())"},{"path":"https://gdrplatform.github.io/gDRimport/reference/load_results_EnVision.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Load EnVision results from xlsx — load_results_EnVision","text":"results_file character vector containing file path(s) results file(s) headers list headers identified manifest","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/load_results_EnVision.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Load EnVision results from xlsx — load_results_EnVision","text":"data.table results data","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/load_results_Tecan.html","id":null,"dir":"Reference","previous_headings":"","what":"Load tecan results from xlsx — load_results_Tecan","title":"Load tecan results from xlsx — load_results_Tecan","text":"functions loads checks results file","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/load_results_Tecan.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Load tecan results from xlsx — load_results_Tecan","text":"","code":"load_results_Tecan(results_file, headers = gDRutils::get_env_identifiers())"},{"path":"https://gdrplatform.github.io/gDRimport/reference/load_results_Tecan.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Load tecan results from xlsx — load_results_Tecan","text":"results_file string, file path result file headers list headers identified manifest","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/load_results_Tecan.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Load tecan results from xlsx — load_results_Tecan","text":"data.table derived Tecan data","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/load_results_tsv.html","id":null,"dir":"Reference","previous_headings":"","what":"Load results from tsv — load_results_tsv","title":"Load results from tsv — load_results_tsv","text":"functions loads checks results file(s)","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/load_results_tsv.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Load results from tsv — load_results_tsv","text":"","code":"load_results_tsv(results_file, headers)"},{"path":"https://gdrplatform.github.io/gDRimport/reference/load_results_tsv.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Load results from tsv — load_results_tsv","text":"results_file character, file path(s) template(s) headers list headers identified manifest","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/load_results_tsv.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Load results from tsv — load_results_tsv","text":"data.table results data","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/load_templates.html","id":null,"dir":"Reference","previous_headings":"","what":"Load templates — load_templates","title":"Load templates — load_templates","text":"functions loads checks template file(s)","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/load_templates.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Load templates — load_templates","text":"","code":"load_templates(df_template_files)"},{"path":"https://gdrplatform.github.io/gDRimport/reference/load_templates.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Load templates — load_templates","text":"df_template_files data.table, datapaths names results file(s) character file path templates file(s)","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/load_templates.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Load templates — load_templates","text":"data.table templates data","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/load_templates.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Load templates — load_templates","text":"","code":"td <- get_test_data()  t_df <- load_templates(template_path(td)) #> INFO [2024-12-09 10:53:18] Reading Template_7daytreated.xlsx with load_templates_xlsx #> INFO [2024-12-09 10:53:18] Loading Template_7daytreated.xlsx #> INFO [2024-12-09 10:53:19] Loading Template_Untreated.xlsx #> INFO [2024-12-09 10:53:19] Templates loaded successfully!"},{"path":"https://gdrplatform.github.io/gDRimport/reference/load_templates_tsv.html","id":null,"dir":"Reference","previous_headings":"","what":"Load templates from tsv — load_templates_tsv","title":"Load templates from tsv — load_templates_tsv","text":"functions loads checks template file(s)","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/load_templates_tsv.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Load templates from tsv — load_templates_tsv","text":"","code":"load_templates_tsv(template_file, template_filename = NULL)"},{"path":"https://gdrplatform.github.io/gDRimport/reference/load_templates_tsv.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Load templates from tsv — load_templates_tsv","text":"template_file character, file path(s) template(s) template_filename character, file name(s)","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/load_templates_tsv.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Load templates from tsv — load_templates_tsv","text":"data.table template data","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/load_templates_xlsx.html","id":null,"dir":"Reference","previous_headings":"","what":"Load templates from xlsx — load_templates_xlsx","title":"Load templates from xlsx — load_templates_xlsx","text":"functions loads checks template file(s)","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/load_templates_xlsx.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Load templates from xlsx — load_templates_xlsx","text":"","code":"load_templates_xlsx(template_file, template_filename = NULL)"},{"path":"https://gdrplatform.github.io/gDRimport/reference/load_templates_xlsx.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Load templates from xlsx — load_templates_xlsx","text":"template_file character, file path(s) template(s) template_filename character, file name(s)","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/load_templates_xlsx.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Load templates from xlsx — load_templates_xlsx","text":"data.table templates data","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/manifest_path-method.html","id":null,"dir":"Reference","previous_headings":"","what":"Method manifest_path — manifest_path","title":"Method manifest_path — manifest_path","text":"Method object gdr_test_data - access slot manifest_path","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/manifest_path-method.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Method manifest_path — manifest_path","text":"","code":"manifest_path(x)  # S4 method for gdr_test_data manifest_path(x)"},{"path":"https://gdrplatform.github.io/gDRimport/reference/manifest_path-method.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Method manifest_path — manifest_path","text":"x object class gdr_test_data","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/manifest_path-method.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Method manifest_path — manifest_path","text":"value slot manifest_path","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/manifest_path-method.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Method manifest_path — manifest_path","text":"","code":"td <- get_test_data()  manifest_file_path <- manifest_path(td)"},{"path":"https://gdrplatform.github.io/gDRimport/reference/mgrepl.html","id":null,"dir":"Reference","previous_headings":"","what":"grep wrapper to support multiple patterns — mgrepl","title":"grep wrapper to support multiple patterns — mgrepl","text":"grep wrapper support multiple patterns","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/mgrepl.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"grep wrapper to support multiple patterns — mgrepl","text":"","code":"mgrepl(patterns, x, do_unlist = TRUE, ...)"},{"path":"https://gdrplatform.github.io/gDRimport/reference/mgrepl.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"grep wrapper to support multiple patterns — mgrepl","text":"patterns charvec patterns checked x charvec data do_unlist logical_flag unlist final results? ... additional argument","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/mgrepl.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"grep wrapper to support multiple patterns — mgrepl","text":"list charvec grep output","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/parse_D300_xml.html","id":null,"dir":"Reference","previous_headings":"","what":"Parse D300 — parse_D300_xml","title":"Parse D300 — parse_D300_xml","text":"function parses D300 *.tdd file (XML format) data.table","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/parse_D300_xml.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Parse D300 — parse_D300_xml","text":"","code":"parse_D300_xml(D300_file)"},{"path":"https://gdrplatform.github.io/gDRimport/reference/parse_D300_xml.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Parse D300 — parse_D300_xml","text":"D300_file string, file path D300 .tdd file","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/parse_D300_xml.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Parse D300 — parse_D300_xml","text":"data.table representing input D300_file.","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/parse_D300_xml.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Parse D300 — parse_D300_xml","text":"","code":"td3 <- get_test_D300_data() fs <- td3[[\"f_96w\"]] dose_df <- parse_D300_xml(fs[[\"d300\"]])"},{"path":"https://gdrplatform.github.io/gDRimport/reference/read_EnVision_delim.html","id":null,"dir":"Reference","previous_headings":"","what":"Read EnVision delimited text files — read_EnVision_delim","title":"Read EnVision delimited text files — read_EnVision_delim","text":"function reads file EnVision Workstation","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/read_EnVision_delim.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read EnVision delimited text files — read_EnVision_delim","text":"","code":"read_EnVision_delim(file, nrows = 10000, seps = c(\",\", \"\\t\"))"},{"path":"https://gdrplatform.github.io/gDRimport/reference/read_EnVision_delim.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read EnVision delimited text files — read_EnVision_delim","text":"file string path input file EnVision scanner nrows maximum number file rows processed seps potential field separators input file","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/read_EnVision_delim.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Read EnVision delimited text files — read_EnVision_delim","text":"list containing data table, n_col, n_row, edited","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/read_EnVision_xlsx.html","id":null,"dir":"Reference","previous_headings":"","what":"Read in single xlsx data from EnVision — read_EnVision_xlsx","title":"Read in single xlsx data from EnVision — read_EnVision_xlsx","text":"Read single xlsx data EnVision","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/read_EnVision_xlsx.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read in single xlsx data from EnVision — read_EnVision_xlsx","text":"","code":"read_EnVision_xlsx(results_file, results_sheet)"},{"path":"https://gdrplatform.github.io/gDRimport/reference/read_EnVision_xlsx.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read in single xlsx data from EnVision — read_EnVision_xlsx","text":"results_file character, file path(s) results file(s) results_sheet results sheet names","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/read_EnVision_xlsx.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Read in single xlsx data from EnVision — read_EnVision_xlsx","text":"data.table results data","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/read_excel_to_dt.html","id":null,"dir":"Reference","previous_headings":"","what":"Read excel file and transorm it into data.table object — read_excel_to_dt","title":"Read excel file and transorm it into data.table object — read_excel_to_dt","text":"Read excel file transorm data.table object","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/read_excel_to_dt.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read excel file and transorm it into data.table object — read_excel_to_dt","text":"","code":"read_excel_to_dt(path, ...)"},{"path":"https://gdrplatform.github.io/gDRimport/reference/read_excel_to_dt.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read excel file and transorm it into data.table object — read_excel_to_dt","text":"path path excel file ... arguments passed readxl::read_excel","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/read_excel_to_dt.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Read excel file and transorm it into data.table object — read_excel_to_dt","text":"data.table object read excel file","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/read_excel_to_dt.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Read excel file and transorm it into data.table object — read_excel_to_dt","text":"","code":"datasets <- readxl::readxl_example(\"datasets.xlsx\") read_excel_to_dt(datasets) #>      Sepal.Length Sepal.Width Petal.Length Petal.Width   Species #>             <num>       <num>        <num>       <num>    <char> #>   1:          5.1         3.5          1.4         0.2    setosa #>   2:          4.9         3.0          1.4         0.2    setosa #>   3:          4.7         3.2          1.3         0.2    setosa #>   4:          4.6         3.1          1.5         0.2    setosa #>   5:          5.0         3.6          1.4         0.2    setosa #>  ---                                                             #> 146:          6.7         3.0          5.2         2.3 virginica #> 147:          6.3         2.5          5.0         1.9 virginica #> 148:          6.5         3.0          5.2         2.0 virginica #> 149:          6.2         3.4          5.4         2.3 virginica #> 150:          5.9         3.0          5.1         1.8 virginica"},{"path":"https://gdrplatform.github.io/gDRimport/reference/read_in_EnVision_file.html","id":null,"dir":"Reference","previous_headings":"","what":"Read EnVision file — read_in_EnVision_file","title":"Read EnVision file — read_in_EnVision_file","text":"function reads file EnVision Workstation","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/read_in_EnVision_file.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read EnVision file — read_in_EnVision_file","text":"","code":"read_in_EnVision_file(file, nrows, seps)"},{"path":"https://gdrplatform.github.io/gDRimport/reference/read_in_EnVision_file.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read EnVision file — read_in_EnVision_file","text":"file input file EnVision nrows maximum number file rows processed seps potential field separators input file","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/read_in_EnVision_file.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Read EnVision file — read_in_EnVision_file","text":"list one element per EnVisoin input file","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/read_in_manifest_file.html","id":null,"dir":"Reference","previous_headings":"","what":"read manifest files — read_in_manifest_file","title":"read manifest files — read_in_manifest_file","text":"read manifest files","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/read_in_manifest_file.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"read manifest files — read_in_manifest_file","text":"","code":"read_in_manifest_file(manifest_file, available_formats)"},{"path":"https://gdrplatform.github.io/gDRimport/reference/read_in_manifest_file.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"read manifest files — read_in_manifest_file","text":"manifest_file character, file path(s) manifest(s) available_formats charvec available file formats","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/read_in_manifest_file.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"read manifest files — read_in_manifest_file","text":"data.table manifest data","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/read_in_result_files.html","id":null,"dir":"Reference","previous_headings":"","what":"Read in results files — read_in_result_files","title":"Read in results files — read_in_result_files","text":"Read results files","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/read_in_result_files.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read in results files — read_in_result_files","text":"","code":"read_in_result_files(results_file, results_filename, headers)"},{"path":"https://gdrplatform.github.io/gDRimport/reference/read_in_result_files.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read in results files — read_in_result_files","text":"results_file data.table, datapaths names results file(s) character file path results file(s) results_filename charvect file names headers list headers identified result files","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/read_in_result_files.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Read in results files — read_in_result_files","text":"data.table results data","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/read_in_results_Tecan.html","id":null,"dir":"Reference","previous_headings":"","what":"read in Tecan data — read_in_results_Tecan","title":"read in Tecan data — read_in_results_Tecan","text":"read Tecan data","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/read_in_results_Tecan.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"read in Tecan data — read_in_results_Tecan","text":"","code":"read_in_results_Tecan(results_file, results_sheets, headers)"},{"path":"https://gdrplatform.github.io/gDRimport/reference/read_in_results_Tecan.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"read in Tecan data — read_in_results_Tecan","text":"results_file string, file path result file results_sheets template sheet names headers list headers identified manifest","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/read_in_results_Tecan.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"read in Tecan data — read_in_results_Tecan","text":"data.table derived Tecan data","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/read_in_template_sheet_xlsx.html","id":null,"dir":"Reference","previous_headings":"","what":"Read in data from xlsx template sheet — read_in_template_sheet_xlsx","title":"Read in data from xlsx template sheet — read_in_template_sheet_xlsx","text":"Read data xlsx template sheet","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/read_in_template_sheet_xlsx.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read in data from xlsx template sheet — read_in_template_sheet_xlsx","text":"","code":"read_in_template_sheet_xlsx(template_file, template_sheets, idx, plate_info)"},{"path":"https://gdrplatform.github.io/gDRimport/reference/read_in_template_sheet_xlsx.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read in data from xlsx template sheet — read_in_template_sheet_xlsx","text":"template_file character, file path(s) template(s) template_sheets template sheet names idx template file index plate_info list plate info","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/read_in_template_sheet_xlsx.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Read in data from xlsx template sheet — read_in_template_sheet_xlsx","text":"data.table template data","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/read_in_template_xlsx.html","id":null,"dir":"Reference","previous_headings":"","what":"Read in xlsx template files — read_in_template_xlsx","title":"Read in xlsx template files — read_in_template_xlsx","text":"Read xlsx template files","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/read_in_template_xlsx.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read in xlsx template files — read_in_template_xlsx","text":"","code":"read_in_template_xlsx(template_file, template_filename, template_sheets)"},{"path":"https://gdrplatform.github.io/gDRimport/reference/read_in_template_xlsx.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read in xlsx template files — read_in_template_xlsx","text":"template_file character, file path(s) template(s) template_filename character, file name(s) template_sheets template sheet names","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/read_in_template_xlsx.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Read in xlsx template files — read_in_template_xlsx","text":"data.table templates data","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/read_in_tsv_template_files.html","id":null,"dir":"Reference","previous_headings":"","what":"read in tsv template files — read_in_tsv_template_files","title":"read in tsv template files — read_in_tsv_template_files","text":"read tsv template files","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/read_in_tsv_template_files.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"read in tsv template files — read_in_tsv_template_files","text":"","code":"read_in_tsv_template_files(template_file, template_filename, templates)"},{"path":"https://gdrplatform.github.io/gDRimport/reference/read_in_tsv_template_files.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"read in tsv template files — read_in_tsv_template_files","text":"template_file character, file path(s) template(s) template_filename character, file name(s) templates list templates data","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/read_in_tsv_template_files.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"read in tsv template files — read_in_tsv_template_files","text":"data.table templates data","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/read_ref_data.html","id":null,"dir":"Reference","previous_headings":"","what":"read_ref_data — read_ref_data","title":"read_ref_data — read_ref_data","text":"Read reference data","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/read_ref_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"read_ref_data — read_ref_data","text":"","code":"read_ref_data(inDir, prefix = \"ref\")"},{"path":"https://gdrplatform.github.io/gDRimport/reference/read_ref_data.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"read_ref_data — read_ref_data","text":"inDir directory path reference data prefix prefix reference file names ('ref' default)","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/read_ref_data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"read_ref_data — read_ref_data","text":"list reference data","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/result_path-method.html","id":null,"dir":"Reference","previous_headings":"","what":"Method result_path — result_path","title":"Method result_path — result_path","text":"Method object gdr_test_data - access slot result_path","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/result_path-method.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Method result_path — result_path","text":"","code":"result_path(x)  # S4 method for gdr_test_data result_path(x)"},{"path":"https://gdrplatform.github.io/gDRimport/reference/result_path-method.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Method result_path — result_path","text":"x object class gdr_test_data","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/result_path-method.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Method result_path — result_path","text":"value slot result_path","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/result_path-method.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Method result_path — result_path","text":"","code":"td <- get_test_data()  result_file_path <- result_path(td)"},{"path":"https://gdrplatform.github.io/gDRimport/reference/save_drug_info_per_well.html","id":null,"dir":"Reference","previous_headings":"","what":"for each drug create a Gnumber and Concentration information for each well — save_drug_info_per_well","title":"for each drug create a Gnumber and Concentration information for each well — save_drug_info_per_well","text":"drug create Gnumber Concentration information well","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/save_drug_info_per_well.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"for each drug create a Gnumber and Concentration information for each well — save_drug_info_per_well","text":"","code":"save_drug_info_per_well(trt_info, trt_gnumber_conc, wb, idfs)"},{"path":"https://gdrplatform.github.io/gDRimport/reference/save_drug_info_per_well.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"for each drug create a Gnumber and Concentration information for each well — save_drug_info_per_well","text":"trt_info list treatment info trt_gnumber_conc list treatment data wb pointer xlsx workbook idfs charvec identifiers","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/save_drug_info_per_well.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"for each drug create a Gnumber and Concentration information for each well — save_drug_info_per_well","text":"NULL invisibly.","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/setEnvForPSet.html","id":null,"dir":"Reference","previous_headings":"","what":"Adjust environment variables to meet gDR standards — setEnvForPSet","title":"Adjust environment variables to meet gDR standards — setEnvForPSet","text":"Adjust environment variables meet gDR standards","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/setEnvForPSet.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Adjust environment variables to meet gDR standards — setEnvForPSet","text":"","code":"setEnvForPSet()"},{"path":"https://gdrplatform.github.io/gDRimport/reference/setEnvForPSet.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Adjust environment variables to meet gDR standards — setEnvForPSet","text":"NULL","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/setEnvForPSet.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Adjust environment variables to meet gDR standards — setEnvForPSet","text":"","code":"setEnvForPSet() gDRutils::reset_env_identifiers()"},{"path":"https://gdrplatform.github.io/gDRimport/reference/standardize_record_values.html","id":null,"dir":"Reference","previous_headings":"","what":"standardize_record_values — standardize_record_values","title":"standardize_record_values — standardize_record_values","text":"map values dictionary","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/standardize_record_values.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"standardize_record_values — standardize_record_values","text":"","code":"standardize_record_values(x, dictionary = DICTIONARY)"},{"path":"https://gdrplatform.github.io/gDRimport/reference/standardize_record_values.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"standardize_record_values — standardize_record_values","text":"x named array dictionary named array","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/standardize_record_values.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"standardize_record_values — standardize_record_values","text":"named array updated names","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/standardize_record_values.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"standardize_record_values — standardize_record_values","text":"","code":"standardize_record_values(c(\"Vehicle\", \"vehcle\")) #> [1] \"vehicle\" \"vehicle\""},{"path":"https://gdrplatform.github.io/gDRimport/reference/template_path-method.html","id":null,"dir":"Reference","previous_headings":"","what":"Method template_path — template_path","title":"Method template_path — template_path","text":"Method object gdr_test_data - access slot template_path","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/template_path-method.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Method template_path — template_path","text":"","code":"template_path(x)  # S4 method for gdr_test_data template_path(x)"},{"path":"https://gdrplatform.github.io/gDRimport/reference/template_path-method.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Method template_path — template_path","text":"x object class gdr_test_data","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/template_path-method.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Method template_path — template_path","text":"value slot template_path","code":""},{"path":"https://gdrplatform.github.io/gDRimport/reference/template_path-method.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Method template_path — template_path","text":"","code":"td <- get_test_data()  template_file_path <- template_path(td)"},{"path":"https://gdrplatform.github.io/gDRimport/reference/validate_template_xlsx.html","id":null,"dir":"Reference","previous_headings":"","what":"Validate template xlsx data — validate_template_xlsx","title":"Validate template xlsx data — validate_template_xlsx","text":"Validate template xlsx 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