add HGG_fusion_evidence and HGG_fusion_counts in molecular_subtype.tsv

analyses/molecular-subtyping-HGG/05-HGG-molecular-subtyping-fusion.Rmd

@@ -92,13 +92,20 @@ The gene fusion with _ROS1_, _ALK_ and _MET_ are added into the output
 
 ```{r}
 
+RTK_list <- c("FGFR1", "NTRK", "MET", "ROS1", "ALK")
+
 summary_df <- fusion_hgg %>%
+  mutate(HGG_Fusion_evidence = apply(.[,colnames(.)[grepl(paste(RTK_list, collapse = "|"), colnames(.))]], 1, FUN =  function(x) {paste(names(x)[x == 1],collapse="/")})) %>%
+  mutate(HGG_Fusion_counts = apply(.[,colnames(.)[grepl(paste(RTK_list, collapse = "|"), colnames(.))]], 1, FUN =  function(x) {length(names(x)[x == 1])})) %>%
   mutate(NTRK_fusions = apply(.[,colnames(.)[grepl("NTRK", colnames(.))]], 1, FUN =  function(x) {paste(names(x)[x == 1],collapse="/")})) %>% 
   mutate(MET_fusions = apply(.[,colnames(.)[grepl("MET", colnames(.))]], 1, FUN =  function(x) {paste(names(x)[x == 1],collapse="/")})) %>% 
   mutate(ROS1_fusions = apply(.[,colnames(.)[grepl("ROS1", colnames(.))]], 1, FUN =  function(x) {paste(names(x)[x == 1],collapse="/")})) %>% 
   mutate(ALK_fusions = apply(.[,colnames(.)[grepl("ALK", colnames(.))]], 1, FUN =  function(x) {paste(names(x)[x == 1],collapse="/")})) %>% 
   mutate(FGFR1_fusions = apply(.[,colnames(.)[grepl("FGFR1", colnames(.))]], 1, FUN =  function(x) {paste(names(x)[x == 1],collapse="/")})) %>% 
-  select(c("Kids_First_Biospecimen_ID", "NTRK_fusions", "MET_fusions", "ROS1_fusions", "ALK_fusions", "FGFR1_fusions"))
+  select(c("Kids_First_Biospecimen_ID", "NTRK_fusions", "MET_fusions", "ROS1_fusions", "ALK_fusions", "FGFR1_fusions", "HGG_Fusion_evidence", "HGG_Fusion_counts")) %>% 
+  dplyr::arrange(Kids_First_Biospecimen_ID)
+
+summary_df[summary_df == ""] = "None"
 
 head(summary_df[order(summary_df$FGFR1_fusions),])
 ```
@@ -115,8 +122,6 @@ To retain information about which gene we're talking about we will include the f
 Write file.
 
 ```{r}
-summary_df[summary_df == ""] = "None"
-
 summary_df %>% 
   write_tsv(output_file)
 ```

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

@@ -147,7 +147,7 @@ What are they?
 
 ```{r}
 missing_bsids <- setdiff(exp_df$Kids_First_Biospecimen_ID,
-                         fusion_df$Sample)
+                         fusion_df$Kids_First_Biospecimen_ID)
 
 histologies_df %>%
   filter(Kids_First_Biospecimen_ID %in% missing_bsids)
@@ -211,8 +211,7 @@ rm(arriba_df, putative_oncogenic_df, starfusion_df, missing_bsids)
 ### Join the Expression and Fusion Data
 
 ```{r}
-rna_df <- left_join(exp_df, fusion_df,
-                    by = c("Kids_First_Biospecimen_ID" = "Sample"))
+rna_df <- left_join(exp_df, fusion_df)
 head(rna_df, n = 10)
 ```
 
@@ -301,12 +300,19 @@ rna_df <- rna_df %>%
 
 
 ### All Data
+Add methylation Kids_First_Biospecimen_ID into all_data_df
 
 ```{r}
+methy_df <- histologies_df %>% 
+  filter(experimental_strategy == "Methylation") %>% 
+  select(Kids_First_Biospecimen_ID, sample_id) %>% 
+  rename("Kids_First_Biospecimen_ID_methy" = "Kids_First_Biospecimen_ID")
+
 all_data_df <- full_join(dna_df, rna_df,
                          by = c("Kids_First_Participant_ID",
                                 "sample_id","cell_line_composition"),
                          suffix = c("_DNA", "_RNA")) %>%
+  left_join(methy_df, by = "sample_id") %>% 
   select(starts_with("Kids_First"), sample_id, everything())
 
 head(all_data_df, n = 10)
@@ -572,8 +578,7 @@ molecular_subtype_table <- bind_rows(h3_g35_df_biospecimen,
 molecular_subtype_table <- all_data_df %>%
   select(Kids_First_Participant_ID, 
          sample_id,
-         Kids_First_Biospecimen_ID_DNA, 
-         Kids_First_Biospecimen_ID_RNA, 
+         starts_with("Kids_First_Biospecimen"),
          composition) %>%
   left_join(molecular_subtype_table) %>%
   distinct() %>%
@@ -607,21 +612,24 @@ molecular_subtype_table <- all_data_df %>%
 
 ```{r}
 NTRK <- fusion_df %>% 
-  select(c("Sample", "NTRK_fusions")) %>%
+  select(Kids_First_Biospecimen_ID, NTRK_fusions) %>%
   filter(NTRK_fusions != "None") %>%
-  pull(Sample) 
+  pull(Kids_First_Biospecimen_ID) 
 
 ALK <- fusion_df %>% 
-  select(c("Sample", "ALK_fusions")) %>% 
-  pull(Sample) 
+  select(Kids_First_Biospecimen_ID, ALK_fusions) %>%
+  filter(ALK_fusions != "None") %>%
+  pull(Kids_First_Biospecimen_ID) 
 
 ROS1 <- fusion_df %>% 
-  select(c("Sample", "ROS1_fusions")) %>% 
-  pull(Sample) 
+  select(Kids_First_Biospecimen_ID, ROS1_fusions) %>%
+  filter(ROS1_fusions != "None") %>%
+  pull(Kids_First_Biospecimen_ID) 
 
 MET <- fusion_df %>% 
-  select(c("Sample", "MET_fusions")) %>% 
-  pull(Sample) 
+  select(Kids_First_Biospecimen_ID, MET_fusions) %>%
+  filter(MET_fusions != "None") %>%
+  pull(Kids_First_Biospecimen_ID) 
 
 
 RTK_list <- c(NTRK, ALK, MET, ROS1)
@@ -634,16 +642,20 @@ IGH <- histologies_df %>%
 IGH <- IGH %>% 
   mutate(molecular_subtype = case_when(
     Kids_First_Biospecimen_ID_DNA %in% NTRK | 
-      Kids_First_Biospecimen_ID_RNA %in% NTRK ~ "IHG, NTRK-altered", 
+      Kids_First_Biospecimen_ID_RNA %in% NTRK |
+      Kids_First_Biospecimen_ID_methy %in% NTRK ~ "IHG, NTRK-altered", 
     
     Kids_First_Biospecimen_ID_DNA %in% ALK | 
-      Kids_First_Biospecimen_ID_RNA %in% ALK ~ "IHG, ALK-altered", 
+      Kids_First_Biospecimen_ID_RNA %in% ALK |
+      Kids_First_Biospecimen_ID_methy %in% ALK ~ "IHG, ALK-altered", 
     
     Kids_First_Biospecimen_ID_DNA %in% ROS1 | 
-      Kids_First_Biospecimen_ID_RNA %in% ROS1 ~ "IHG, ROS1-altered", 
+      Kids_First_Biospecimen_ID_RNA %in% ROS1 |
+      Kids_First_Biospecimen_ID_methy %in% ROS1 ~ "IHG, ROS1-altered", 
     
     Kids_First_Biospecimen_ID_DNA %in% MET | 
-      Kids_First_Biospecimen_ID_RNA %in% MET ~ "IHG, MET-altered", 
+      Kids_First_Biospecimen_ID_RNA %in% MET |
+      Kids_First_Biospecimen_ID_methy %in% MET ~ "IHG, MET-altered", 
     
     !(Kids_First_Biospecimen_ID_DNA %in% RTK_list) & 
       !(Kids_First_Biospecimen_ID_RNA %in% RTK_list) &
@@ -667,15 +679,17 @@ IGH <- IGH %>%
   
   select(c(Kids_First_Participant_ID, 
            sample_id, 
-           Kids_First_Biospecimen_ID_DNA, 
+           starts_with("Kids_First_Biospecimen"), 
            Kids_First_Biospecimen_ID_RNA, 
            molecular_subtype, 
-           composition)) %>% 
+           composition, 
+           HGG_Fusion_evidence, 
+           HGG_Fusion_counts)) %>% 
   
   filter(molecular_subtype != "delete") %>% 
   unique()
 
-molecular_subtype_table <-molecular_subtype_table %>% 
+molecular_subtype_table <- molecular_subtype_table %>% 
   filter(!sample_id %in% IGH$sample_id) %>%
   bind_rows(IGH) 
 

analyses/molecular-subtyping-HGG/10-HGG-TP53-annotation.Rmd

@@ -49,10 +49,12 @@ hgg_subtypes <- hgg_subtypes %>%
                              "Kids_First_Biospecimen_ID_DNA")) %>%
   rename("tp53_SNV_indel_counts"="SNV_indel_counts",
          "tp53_CNV_loss_counts"="CNV_loss_counts",
-          "tp53_HGVSp_Short"="HGVSp_Short" , 
+         "tp53_HGVSp_Short"="HGVSp_Short" , 
          "tp53_CNV_loss_evidence"="CNV_loss_evidence",
          "tp53_hotspot"="hotspot",
-         "tp53_activating"="activating") %>%
+         "tp53_activating"="activating",
+         "tp53_Fusion_counts"="Fusion_counts", 
+         "tp53_Fusion_evidence"="Fusion_evidence") %>%
   mutate(molecular_subtype= case_when(
     tp53_altered=="activated" ~ stringr::str_c(molecular_subtype,", TP53 activated"),
     tp53_altered=="loss" ~ stringr::str_c(molecular_subtype,", TP53 loss"),

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

@@ -1841,15 +1841,18 @@ <h3>Required files</h3>
 
 hgg_subtypes &lt;- read_tsv(file.path(results_dir,&quot;HGG_molecular_subtype.tsv&quot;)) </code></pre>
 <!-- rnb-source-end -->
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 <pre><code>Parsed with column specification:
 cols(
   Kids_First_Participant_ID = col_character(),
   sample_id = col_character(),
   Kids_First_Biospecimen_ID_DNA = col_character(),
   Kids_First_Biospecimen_ID_RNA = col_character(),
+  Kids_First_Biospecimen_ID_methy = col_character(),
   composition = col_character(),
-  molecular_subtype = col_character()
+  molecular_subtype = col_character(),
+  HGG_Fusion_evidence = col_character(),
+  HGG_Fusion_counts = col_double()
 )</code></pre>
 <!-- rnb-message-end -->
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@@ -1863,18 +1866,20 @@ <h3>Required files</h3>
 <h1>Add tp53 status</h1>
 <!-- rnb-text-end -->
 <!-- rnb-chunk-begin -->
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 <pre class="r"><code>hgg_subtypes &lt;- hgg_subtypes %&gt;%
   left_join(tp53_status,by=c(
                              &quot;sample_id&quot;,
                              &quot;Kids_First_Biospecimen_ID_RNA&quot;,
                              &quot;Kids_First_Biospecimen_ID_DNA&quot;)) %&gt;%
   rename(&quot;tp53_SNV_indel_counts&quot;=&quot;SNV_indel_counts&quot;,
          &quot;tp53_CNV_loss_counts&quot;=&quot;CNV_loss_counts&quot;,
-          &quot;tp53_HGVSp_Short&quot;=&quot;HGVSp_Short&quot; , 
+         &quot;tp53_HGVSp_Short&quot;=&quot;HGVSp_Short&quot; , 
          &quot;tp53_CNV_loss_evidence&quot;=&quot;CNV_loss_evidence&quot;,
          &quot;tp53_hotspot&quot;=&quot;hotspot&quot;,
-         &quot;tp53_activating&quot;=&quot;activating&quot;) %&gt;%
+         &quot;tp53_activating&quot;=&quot;activating&quot;,
+         &quot;tp53_Fusion_counts&quot;=&quot;Fusion_counts&quot;, 
+         &quot;tp53_Fusion_evidence&quot;=&quot;Fusion_evidence&quot;) %&gt;%
   mutate(molecular_subtype= case_when(
     tp53_altered==&quot;activated&quot; ~ stringr::str_c(molecular_subtype,&quot;, TP53 activated&quot;),
     tp53_altered==&quot;loss&quot; ~ stringr::str_c(molecular_subtype,&quot;, TP53 loss&quot;),
@@ -1886,7 +1891,7 @@ <h1>Add tp53 status</h1>
 <!-- rnb-chunk-end -->
 </div>
 
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