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Previously missing PB subtypes added #601

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Aug 16, 2024
Merged

Previously missing PB subtypes added #601

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4caff92
Previously missing PB subtypes added
sangeetashukla Jul 22, 2024
e681630
Removed additional subtypes per comments on OPC PR601
sangeetashukla Aug 6, 2024
638b8f3
fix bug where methyl subtype existed when low conf
jharenza Aug 15, 2024
75aaad6
🧱 Increase size for analysis job
devbyaccident Aug 15, 2024
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17 changes: 14 additions & 3 deletions analyses/molecular-subtyping-PB/01-molecular-subtype-pineoblastoma.Rmd
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Original file line number Diff line number Diff line change
Expand Up @@ -46,7 +46,10 @@ pb_meta <- histo %>%
dkfz_v12_methylation_subclass == "PIN_RB" ~ "PB, RB1",
dkfz_v12_methylation_subclass == "PB_GRP1A" ~ "PB, Group 1A",
dkfz_v12_methylation_subclass == "PB_GRP1B" ~ "PB, Group 1B",
dkfz_v12_methylation_subclass == "PB_GRP2" ~ "PB, Group 2"))
dkfz_v12_methylation_subclass == "PB_GRP2" ~ "PB, Group 2",
dkfz_v12_methylation_subclass == "PPTID_A" ~ "PB, PPTID"
))


```

Expand All @@ -62,19 +65,27 @@ pb_meta <- histo %>%
## PB_GRP2: pineoblastoma, miRNA processing-altered 2 (PB, Group 2)
## PIN_RB: pineoblastoma, RB1-altered (PB, RB1)

## Additional subtypes added on 07/22/2024
## Edited By: Sangeeta Shukla
## PPTID_A: Pineal Parenchymal Tumor of Intermediate Differentiation Type A


```{r}

pb_methy_with_subtype <- pb_meta %>%
filter(experimental_strategy == "Methylation" & dkfz_v12_methylation_subclass_score >= 0.8) %>%
mutate(molecular_subtype = case_when(molecular_subtype_methyl == "PB, MYC/FOXR2" ~ "PB, MYC/FOXR2",
molecular_subtype_methyl == "PB, RB1" ~ "PB, RB1",
molecular_subtype_methyl %in% c("PB, Group 1A", "PB, Group 1B") ~ "PB, Group 1",
molecular_subtype_methyl == "PB, Group 2" ~ "PB, Group 2"))
molecular_subtype_methyl == "PB, Group 2" ~ "PB, Group 2",
molecular_subtype_methyl == "PPTID" ~ "PB, PPTID"
))


pb_methy_without_subtype <- pb_meta %>%
filter(experimental_strategy == "Methylation" &
!(Kids_First_Biospecimen_ID %in% pb_methy_with_subtype$Kids_First_Biospecimen_ID))
!(Kids_First_Biospecimen_ID %in% pb_methy_with_subtype$Kids_First_Biospecimen_ID)) %>%
mutate(molecular_subtype_methyl = NA_character_)

pb_methyl_df <- pb_methy_with_subtype %>%
bind_rows(pb_methy_without_subtype) %>%
Expand Down
78 changes: 48 additions & 30 deletions analyses/molecular-subtyping-PB/01-molecular-subtype-pineoblastoma.html
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Original file line number Diff line number Diff line change
Expand Up @@ -360,13 +360,13 @@ <h4 class="date">2023-12-06</h4>
<div id="load-library" class="section level2">
<h2>load library</h2>
<pre class="r"><code>library(tidyverse)</code></pre>
<pre><code>## ── Attaching core tidyverse packages ─────────────────────────────────────────── tidyverse 2.0.0 ──
## ✔ dplyr 1.1.1 ✔ readr 2.1.4
## ✔ forcats 1.0.0 ✔ stringr 1.5.0
## ✔ ggplot2 3.4.2 ✔ tibble 3.2.1
## ✔ lubridate 1.9.2 ✔ tidyr 1.3.0
## ✔ purrr 1.0.1
## ── Conflicts ───────────────────────────────────────────────────────────── tidyverse_conflicts() ──
<pre><code>## ── Attaching core tidyverse packages ──────────────────────────────────── tidyverse 2.0.0 ──
## ✔ dplyr 1.1.4 ✔ readr 2.1.5
## ✔ forcats 1.0.0 ✔ stringr 1.5.1
## ✔ ggplot2 3.5.1 ✔ tibble 3.2.1
## ✔ lubridate 1.9.3 ✔ tidyr 1.3.1
## ✔ purrr 1.0.2
## ── Conflicts ────────────────────────────────────────────────────── tidyverse_conflicts() ──
## ✖ dplyr::filter() masks stats::filter()
## ✖ dplyr::lag() masks stats::lag()
## ℹ Use the conflicted package (&lt;http://conflicted.r-lib.org/&gt;) to force all conflicts to become errors</code></pre>
Expand All @@ -385,7 +385,7 @@ <h2>set directories</h2>
<h2>read files</h2>
<pre class="r"><code>histo &lt;- readr::read_tsv(file.path(data_dir, &quot;histologies-base.tsv&quot;))</code></pre>
<pre><code>## Rows: 47895 Columns: 64
## ── Column specification ───────────────────────────────────────────────────────────────────────────
## ── Column specification ────────────────────────────────────────────────────────────────────
## Delimiter: &quot;\t&quot;
## chr (41): Kids_First_Participant_ID, Kids_First_Biospecimen_ID, sample_id, a...
## dbl (21): cell_line_passage, OS_days, EFS_days, age_at_diagnosis_days, age_a...
Expand All @@ -409,7 +409,9 @@ <h2>select PB samples from histologies</h2>
dkfz_v12_methylation_subclass == &quot;PIN_RB&quot; ~ &quot;PB, RB1&quot;,
dkfz_v12_methylation_subclass == &quot;PB_GRP1A&quot; ~ &quot;PB, Group 1A&quot;,
dkfz_v12_methylation_subclass == &quot;PB_GRP1B&quot; ~ &quot;PB, Group 1B&quot;,
dkfz_v12_methylation_subclass == &quot;PB_GRP2&quot; ~ &quot;PB, Group 2&quot;)) </code></pre>
dkfz_v12_methylation_subclass == &quot;PB_GRP2&quot; ~ &quot;PB, Group 2&quot;,
dkfz_v12_methylation_subclass == &quot;PPTID_A&quot; ~ &quot;PB, PPTID&quot;
))</code></pre>
</div>
<div id="there-are-four-subtypes" class="section level2">
<h2>there are four subtypes:</h2>
Expand Down Expand Up @@ -442,17 +444,30 @@ <h2>PB_GRP2: pineoblastoma, miRNA processing-altered 2 (PB, Group
</div>
<div id="pin_rb-pineoblastoma-rb1-altered-pb-rb1" class="section level2">
<h2>PIN_RB: pineoblastoma, RB1-altered (PB, RB1)</h2>
</div>
<div id="additional-subtypes-added-on-07222024" class="section level2">
<h2>Additional subtypes added on 07/22/2024</h2>
</div>
<div id="edited-by-sangeeta-shukla" class="section level2">
<h2>Edited By: Sangeeta Shukla</h2>
</div>
<div id="pptid_a-pineal-parenchymal-tumor-of-intermediate-differentiation-type-a" class="section level2">
<h2>PPTID_A: Pineal Parenchymal Tumor of Intermediate Differentiation
Type A</h2>
<pre class="r"><code>pb_methy_with_subtype &lt;- pb_meta %&gt;%
filter(experimental_strategy == &quot;Methylation&quot; &amp; dkfz_v12_methylation_subclass_score &gt;= 0.8) %&gt;%
mutate(molecular_subtype = case_when(molecular_subtype_methyl == &quot;PB, MYC/FOXR2&quot; ~ &quot;PB, MYC/FOXR2&quot;,
molecular_subtype_methyl == &quot;PB, RB1&quot; ~ &quot;PB, RB1&quot;,
molecular_subtype_methyl %in% c(&quot;PB, Group 1A&quot;, &quot;PB, Group 1B&quot;) ~ &quot;PB, Group 1&quot;,
molecular_subtype_methyl == &quot;PB, Group 2&quot; ~ &quot;PB, Group 2&quot;))
molecular_subtype_methyl == &quot;PB, Group 2&quot; ~ &quot;PB, Group 2&quot;,
molecular_subtype_methyl == &quot;PPTID&quot; ~ &quot;PB, PPTID&quot;
))


pb_methy_without_subtype &lt;- pb_meta %&gt;%
filter(experimental_strategy == &quot;Methylation&quot; &amp;
!(Kids_First_Biospecimen_ID %in% pb_methy_with_subtype$Kids_First_Biospecimen_ID))
!(Kids_First_Biospecimen_ID %in% pb_methy_with_subtype$Kids_First_Biospecimen_ID)) %&gt;%
mutate(molecular_subtype_methyl = NA_character_)

pb_methyl_df &lt;- pb_methy_with_subtype %&gt;%
bind_rows(pb_methy_without_subtype) %&gt;%
Expand All @@ -478,13 +493,13 @@ <h2>assign the molecular subtypes to all samples based on the
<div id="session-info" class="section level2">
<h2>session info</h2>
<pre class="r"><code>sessionInfo()</code></pre>
<pre><code>## R version 4.2.3 (2023-03-15)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 22.04.2 LTS
<pre><code>## R version 4.4.0 (2024-04-24)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 22.04.4 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
## 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
Expand All @@ -494,26 +509,29 @@ <h2>session info</h2>
## [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] lubridate_1.9.2 forcats_1.0.0 stringr_1.5.0 dplyr_1.1.1
## [5] purrr_1.0.1 readr_2.1.4 tidyr_1.3.0 tibble_3.2.1
## [9] ggplot2_3.4.2 tidyverse_2.0.0
## [1] lubridate_1.9.3 forcats_1.0.0 stringr_1.5.1 dplyr_1.1.4
## [5] purrr_1.0.2 readr_2.1.5 tidyr_1.3.1 tibble_3.2.1
## [9] ggplot2_3.5.1 tidyverse_2.0.0
##
## loaded via a namespace (and not attached):
## [1] bslib_0.4.2 compiler_4.2.3 pillar_1.9.0 jquerylib_0.1.4
## [5] tools_4.2.3 bit_4.0.5 digest_0.6.31 timechange_0.2.0
## [9] jsonlite_1.8.4 evaluate_0.20 lifecycle_1.0.3 gtable_0.3.3
## [13] pkgconfig_2.0.3 rlang_1.1.0 cli_3.6.1 parallel_4.2.3
## [17] yaml_2.3.7 xfun_0.38 fastmap_1.1.1 withr_2.5.0
## [21] knitr_1.42 generics_0.1.3 vctrs_0.6.2 sass_0.4.5
## [25] hms_1.1.3 bit64_4.0.5 rprojroot_2.0.3 grid_4.2.3
## [29] tidyselect_1.2.0 glue_1.6.2 R6_2.5.1 fansi_1.0.4
## [33] vroom_1.6.1 rmarkdown_2.21 tzdb_0.3.0 magrittr_2.0.3
## [37] scales_1.2.1 htmltools_0.5.5 colorspace_2.1-0 utf8_1.2.3
## [41] stringi_1.7.12 munsell_0.5.0 cachem_1.0.7 crayon_1.5.2</code></pre>
## [1] bit_4.0.5 gtable_0.3.5 jsonlite_1.8.8 crayon_1.5.2
## [5] compiler_4.4.0 tidyselect_1.2.1 parallel_4.4.0 jquerylib_0.1.4
## [9] scales_1.3.0 yaml_2.3.8 fastmap_1.2.0 R6_2.5.1
## [13] generics_0.1.3 knitr_1.46 rprojroot_2.0.4 munsell_0.5.1
## [17] bslib_0.7.0 pillar_1.9.0 tzdb_0.4.0 rlang_1.1.3
## [21] utf8_1.2.4 stringi_1.8.4 cachem_1.1.0 xfun_0.44
## [25] sass_0.4.9 bit64_4.0.5 timechange_0.3.0 cli_3.6.2
## [29] withr_3.0.0 magrittr_2.0.3 digest_0.6.35 grid_4.4.0
## [33] vroom_1.6.5 hms_1.1.3 lifecycle_1.0.4 vctrs_0.6.5
## [37] evaluate_0.23 glue_1.7.0 fansi_1.0.6 colorspace_2.1-0
## [41] rmarkdown_2.27 tools_4.4.0 pkgconfig_2.0.3 htmltools_0.5.8.1</code></pre>
</div>


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