Update 01_mpnst_get_omics.R

PNNL-CompBio · Jun 20, 2024 · 08fcd78 · 08fcd78
1 parent e4f9354
commit 08fcd78
Showing 1 changed file with 4 additions and 6 deletions.
diff --git a/build/mpnst/01_mpnst_get_omics.R b/build/mpnst/01_mpnst_get_omics.R
@@ -60,10 +60,8 @@ combined<-rbind(pdx_data,tumor_data)|>distinct()
 genes_df <- fread(genefile)
 
 
-
-
 ##added proteomics first
-proteomics<-do.call('rbind',lapply(setdiff(combined$Proteomics,c('',NA)),function(x){
+proteomics<-do.call('rbind',lapply(setdiff(combined$Proteomics,c('',NA,"NA")),function(x){
                                         # if(x!=""){
     #print(x)
     sample<-subset(combined,Proteomics==x)
@@ -90,7 +88,7 @@ fwrite(proteomics,'/tmp/mpnst_proteomics.csv.gz')
 
 #### FIRST WE GET RNASeq Data
 
-rnaseq<-do.call('rbind',lapply(setdiff(combined$RNASeq,NA),function(x){
+rnaseq<-do.call('rbind',lapply(setdiff(combined$RNASeq,NA,"NA"),function(x){
                                         # if(x!=""){
     #print(x)
     sample<-subset(combined,RNASeq==x)
@@ -116,7 +114,7 @@ fwrite(rnaseq,'/tmp/mpnst_transcriptomics.csv.gz')
 
 #####NEXT WE DO WES DATA
 print("Getting WES")
-wes<-do.call(rbind,lapply(setdiff(combined$`Mutations`,NA),function(x){
+wes<-do.call(rbind,lapply(setdiff(combined$`Mutations`,NA,"NA"),function(x){
 
     x2=x#gsub('"','',gsub("[",'',gsub("]",'',x,fixed=T),fixed=T),fixed=T)
     print(x)
@@ -143,7 +141,7 @@ fwrite(wes,'/tmp/mpnst_mutations.csv.gz')
 
 print(paste("getting CNV"))
 ##next let's do CNVs!
-cnv<-do.call(rbind,lapply(setdiff(combined$CopyNumber,NA),function(x){
+cnv<-do.call(rbind,lapply(setdiff(combined$CopyNumber,NA,"NA"),function(x){
 
     x2=x#gsub('"','',gsub("[",'',gsub("]",'',x,fixed=T),fixed=T),fixed=T)
     print(x)