Merge pull request #610 from d3b-center/OPC_607_SS

Manual cancer_group assigned for select sample_id with discordant pathology_diagnosis

analyses/efo-mondo-mapping/results/efo-mondo-map-prefill.tsv

@@ -89,6 +89,7 @@ Myeloid Sarcoma	NA	NA	NA
 Neuroblastoma	EFO_0000621	MONDO_0005072	NCIT_C3270
 Neurofibroma/Plexiform	EFO_0000658	MONDO_0003304	NCIT_C3797
 Non-Hodgkin Lymphoma	EFO_0005952	MONDO_0018908	NCIT_C3211
+Not Reported	NA	NA	NA
 Oligodendroglioma	EFO_0000632	MONDO_0016695	NCIT_C3288
 Osteosarcoma	EFO_0000637	MONDO_0009807	NCIT_C9145
 Other tumor	NA	NA	NA

analyses/molecular-subtyping-HGG/07-HGG-molecular-subtyping-combine-table.Rmd

@@ -544,10 +544,22 @@ to_be_classified <- hgg_meta %>%
   mutate(molecular_subtype = "HGG, To be classified") %>%
 select(Kids_First_Participant_ID, Kids_First_Biospecimen_ID, sample_id, match_id, molecular_subtype)
 
-molecular_subtype_table_final <- all_subtypes %>%
+molecular_subtype_table_w_tbc <- all_subtypes %>%
   bind_rows(to_be_classified) %>%
   arrange(Kids_First_Biospecimen_ID)
 
+# update non DMG brainstem glioma dx to DIPG based on clinical dx for PNOC and Mioncoseq only. 
+# HGG, IDH remain as HGG
+dipgs <- hgg_meta %>%
+  filter(sub_cohort %in% c("PNOC", "Mioncoseq") &
+           grepl("Brainstem glioma", pathology_diagnosis)) %>%
+  select(Kids_First_Biospecimen_ID, primary_site)
+
+molecular_subtype_table_final <- molecular_subtype_table_w_tbc %>%
+  dplyr::mutate(molecular_subtype = case_when(Kids_First_Biospecimen_ID %in% dipgs$Kids_First_Biospecimen_ID & 
+                                                grepl("HGG, H3 wildtype|HGG, To be classified", molecular_subtype) ~ gsub("HGG", "DIPG", molecular_subtype),
+                                              TRUE ~ molecular_subtype))
+  
 # create final lesion + subtype file
 lesions_subtypes <- all_data_df %>%
   right_join(molecular_subtype_table_final[,c("match_id", "molecular_subtype")]) %>%

analyses/molecular-subtyping-HGG/10-HGG-TP53-annotation.nb.html

@@ -1512,7 +1512,7 @@
     $(this).detach().appendTo(div);
 
     // add a show code button right above
-    var showCodeText = $('<span>' + (showThis ? 'Hide' : 'Code') + '</span>');
+    var showCodeText = $('<span>' + (showThis ? 'Hide' : 'Show') + '</span>');
     var showCodeButton = $('<button type="button" class="btn btn-default btn-xs btn-secondary btn-sm code-folding-btn pull-right float-right"></button>');
     showCodeButton.append(showCodeText);
     showCodeButton
@@ -1538,7 +1538,7 @@
     //   * Change text
     //   * add a class for intermediate states styling
     div.on('hide.bs.collapse', function () {
-      showCodeText.text('Code');
+      showCodeText.text('Show');
       showCodeButton.addClass('btn-collapsing');
     });
     div.on('hidden.bs.collapse', function () {
@@ -1766,14 +1766,14 @@ <h2>Set up</h2>
 <pre class="r"><code># Load in tidyverse functions
 library(tidyverse)</code></pre>
 <!-- rnb-source-end -->
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-<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() ──
+<!-- rnb-message-begin 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 -->
+<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>
@@ -1804,9 +1804,9 @@ <h3>Required files</h3>
   &quot;tp53_altered_status.tsv&quot;), guess_max = 100000) %&gt;%
   dplyr::rename(tp53_status = tp53_altered)</code></pre>
 <!-- rnb-source-end -->
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 <pre><code>Rows: 14307 Columns: 18
-── Column specification ───────────────────────────────────────────────────────────────────────────
+── Column specification ──────────────────────────────────────────────────────────────────────────────────────────────────────
 Delimiter: &quot;\t&quot;
 chr (10): Kids_First_Biospecimen_ID, match_id, sample_id, cancer_predisposit...
 dbl  (8): tp53_score, SV_counts, Fusion_counts, SNV_indel_counts, CNV_loss_c...
@@ -1819,9 +1819,9 @@ <h3>Required files</h3>
   filter(!is.na(pathology_diagnosis),
          !cohort %in% c(&quot;TCGA&quot;, &quot;GTEx&quot;))</code></pre>
 <!-- rnb-source-end -->
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 <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...
@@ -1834,9 +1834,9 @@ <h3>Required files</h3>
 <pre class="r"><code>hgg_subtypes &lt;- read_tsv(file.path(results_dir,&quot;HGG_cleaned_all_table.tsv&quot;)) %&gt;%
   left_join(bs_match)</code></pre>
 <!-- rnb-source-end -->
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 <pre><code>Rows: 2155 Columns: 48
-── Column specification ───────────────────────────────────────────────────────────────────────────
+── Column specification ──────────────────────────────────────────────────────────────────────────────────────────────────────
 Delimiter: &quot;\t&quot;
 chr (41): Kids_First_Participant_ID, Kids_First_Biospecimen_ID, sample_id, m...
 dbl  (7): age_at_diagnosis_yr, FOXG1_expression_zscore, OLIG2_expression_zsc...