Gdr 2224

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: gDRutils
 Type: Package
 Title: A package with helper functions for processing drug response data
-Version: 0.99.39
-Date: 2023-11-10
+Version: 0.99.40
+Date: 2023-11-15
 Authors@R: c(person("Bartosz", "Czech", role=c("aut")),
              person("Arkadiusz", "Gladki", role=c("cre", "aut"), email="[email protected]"),
              person("Aleksander", "Chlebowski", role=c("aut")),

NEWS.md

@@ -1,3 +1,7 @@
+## 0.99.40 (2023-11-15)
+- fix bug with refining rowData
+- extend the list of headers
+
 ## 0.99.39 (2023-11-10)
 - update schema to support NA in reference division time
 

R/headers_list.R

@@ -42,6 +42,7 @@
     get_env_identifiers("drug_name", simplify = TRUE),
     get_env_identifiers("masked_tag", simplify = TRUE),
     paste0(get_env_identifiers("drug_name", simplify = TRUE), "_", 2:10),
+    paste0(get_env_identifiers("drug_moa", simplify = TRUE), "_", 2:10),
     HEADERS_LIST[["raw_data"]],
     HEADERS_LIST[["normalized_results"]],
     HEADERS_LIST[["averaged_results"]],
@@ -51,6 +52,22 @@
 
   HEADERS_LIST[["ordered_1"]] <- .orderHeaderList(HEADERS_LIST, 1)
   HEADERS_LIST[["ordered_2"]] <- .orderHeaderList(HEADERS_LIST, 2)
+
+  HEADERS_LIST[["id"]] <- c("rId", "cId")
+
+  HEADERS_LIST[["combo"]] <- c("normalization_type",
+                               "iso_level",
+                               "pos_x",
+                               "pos_y",
+                               "pos_x_ref",
+                               "pos_y_ref",
+                               "log2_CI",
+                               "log10_ratio_conc")
+
+  HEADERS_LIST[["obsolete"]] <- c("RV",
+                                  "GR",
+                                  "Excess")
+
 
   HEADERS_LIST
 }
@@ -83,7 +100,9 @@
 .getAveragedResultsList <- function() {
   c(
     "x",
-    "x_std"
+    "x_std",
+    "std_RelativeViability",
+    "std_GRvalue"
   )
 }
 

R/standardize_MAE.R

@@ -198,13 +198,14 @@ get_optional_coldata_fields <- function(se) {
 #'
 get_optional_rowdata_fields <- function(se) {
   idfs <- get_SE_identifiers(se)
+  rowdata <- SummarizedExperiment::rowData(se)
 
   out <- c(idfs["drug_moa"])
 
-  if (!is.null(idfs["drug2"])) {
+  if (!is.null(rowdata[[idfs[["drug2"]]]])) {
     out <- c(out, idfs["drug_moa2"])
   }
-  if (!is.null(idfs["drug3"])) {
+  if (!is.null(rowdata[[idfs[["drug3"]]]])) {
     out <- c(out, idfs["drug_moa3"])
   }
 

tests/testthat/test-headers.R

@@ -5,7 +5,7 @@ test_that("get_header works", {
   expect_equal(get_header("manifest"), list(barcode = c("Barcode", "Plate"),
                                             template = c("Template", "Treatment"),
                                             duration = "Duration"))
-  expect_equal(length(get_header()), 13)
+  expect_equal(length(get_header()), 14)
 
   set_env_identifier("duration", "TEST_DURATION")
   expect_equal(get_header("manifest"), list(barcode = c("Barcode", "Plate"),