Merge pull request #4 from karissawhiting/development

Make sure genes that have been renamed between panels are consistently coded with updated gene name

R/make-bin-mat.R

@@ -38,6 +38,7 @@ create.bin.matrix <- function(patients=NULL, maf, mut.type = "SOMATIC",SNP.only
   if(length(match("Mutation_Status",colnames(maf))) == 0)
     stop("The MAF file inputted is missing a mutation status column. (Mutation_Status)")
 
+  # recode gene names that have been changed between panel versions to make sure they are consistent and counted as the same gene
   if (sum(grepl("KMT2D", maf$Hugo_Symbol)) > 1) {
     maf <- maf %>%
       mutate(Hugo_Symbol = case_when(
@@ -48,6 +49,16 @@ create.bin.matrix <- function(patients=NULL, maf, mut.type = "SOMATIC",SNP.only
     warning("KMT2D has been recoded to MLL2")
   }
 
+  if (sum(grepl("KMT2C", maf$Hugo_Symbol)) > 1) {
+    maf <- maf %>%
+      mutate(Hugo_Symbol = case_when(
+        Hugo_Symbol == "KMT2C" ~ "MLL3",
+        TRUE ~ Hugo_Symbol
+      ))
+
+    warning("KMT2C has been recoded to MLL3")
+  }
+
   maf <- as.data.frame(maf)
 
   # filter/define patients #