Add plot labels to pbta-histologies.tsv file

Read in clinical data.

clin <- read.delim("~/OpenPBTA-analysis/data/release-v15-20200228/pbta-histologies.tsv", header = T, sep = "\t")

Add medulloblastoma labels.

##If MB samples were not subtyped, retain only integrated diagnosis. If subtyped, concat with subtype
clin$label <- ifelse(clin$integrated_diagnosis == "Medulloblastoma" & !is.na(clin$molecular_subtype),
                       paste0(clin$integrated_diagnosis, "-", clin$molecular_subtype), 
                     ifelse(clin$integrated_diagnosis == "Medulloblastoma" & is.na(clin$molecular_subtype),
                            paste0(clin$integrated_diagnosis), paste0(clin$molecular_subtype)))
##check labels
as.data.frame(table(clin$label))

Add ATRT labels.

##Since ATRT has a broad_histology == Embryonal Tumor, we should specify the disease type in the label
clin$label <- unlist(ifelse(clin$short_histology == "ATRT", 
                            paste0(clin$short_histology), paste0(clin$label)))
##check labels
as.data.frame(table(clin$label))

For “Other” tumors, use integrated diagnosis.

This results in a lot of histologies of small N - discuss what we would like to see here.

clin$label <- unlist(ifelse(clin$short_histology == "Other", 
                            paste0(clin$integrated_diagnosis), paste0(clin$label)))
##check labels
as.data.frame(table(clin$label))

Fix NAs - some NAs are converted to factors when the above is done (there may be a way to stop this during ifelse, but couldn’t quickly find).

clin$label <- ifelse(clin$label == "NA", NA, paste0(clin$label))

For remaining samples, use broad_histology for missing labels.

clin$label <- ifelse(is.na(clin$label), 
                     paste0(clin$short_histology), paste0(clin$label))
## Check all labels
as.data.frame(table(clin$label))

A few notes:

• The 833 remaining NAs are the normal specimens.
• The CNS EFT-CIC will become CNS Ewings sarcoma.
• We have a standalone BRAF V600E subtype, but this is HGG only, and should be labeled as such.
• We probably want to label LGAT as LGG BRAF fusion, LGG BRAF V600E, or LGG BRAF WT.