Integrate surface and nuclear protein localization into DEG generation

r.scripts/sc_DEG.R

@@ -35,6 +35,14 @@ load(paste0("./analysis/sc10x.",Project.Name,".",opt$g,".cluster.IDStress.Rda"))
 sc10x.Group.Stress <- get(paste0("sc10x.",opt$g,".cluster.IDStress"))
 rm(list=paste0("sc10x.",opt$g,".cluster.IDStress"))
 
+#open nuclear/surface protein gene lists
+surface <- read_delim("./genesets/uniprot-keyword_huCellMembrane.tab","\t",escape_double=FALSE,trim_ws=TRUE)
+surface <- surface[[2]]
+surface <- surface[complete.cases(surface)]
+nuclear <- read_delim("./genesets/uniprot-location_huNuclear.tab","\t",escape_double=FALSE,trim_ws=TRUE)
+nuclear <- nuclear[[2]]
+nuclear <- nuclear[complete.cases(nuclear)]
+
 #create folder structure
 if (!dir.exists(paste0("./analysis/",opt$g))){
   dir.create(paste0("./analysis/",opt$g))
@@ -172,6 +180,16 @@ rm(DEG)
 
 for (i in ls(pattern="^DEG")){
   write.table(get(i),file=paste0("./analysis/",opt$g,"/global/DEG/",i,".csv"),row.names=TRUE,col.names=NA,append=FALSE,sep=",")
+  write.table(get(i) %in% surface[,2],file=paste0("./analysis/",opt$g,"/global/DEG/",i,".surface.csv"),row.names=TRUE,col.names=NA,append=FALSE,sep=",")
+}
+
+for (i in ls(pattern="^DEG\\.")){
+  write.table(get(i)[rownames(get(i)) %in% surface,],file=paste0("./analysis/",opt$g,"/global/DEG/",i,".surface.csv"),row.names=TRUE,col.names=NA,append=FALSE,sep=",")
+  write.table(get(i)[rownames(get(i)) %in% nuclear,],file=paste0("./analysis/",opt$g,"/global/DEG/",i,".nuclear.csv"),row.names=TRUE,col.names=NA,append=FALSE,sep=",")
+}
+for (i in ls(pattern="^DEG_")){
+  write.table(get(i)[get(i) %in% surface],file=paste0("./analysis/",opt$g,"/global/DEG/",i,".surface.csv"),row.names=TRUE,col.names=NA,append=FALSE,sep=",")
+  write.table(get(i)[get(i) %in% nuclear],file=paste0("./analysis/",opt$g,"/global/DEG/",i,".nuclear.csv"),row.names=TRUE,col.names=NA,append=FALSE,sep=",")
 }
 
 cat(row.names(DEG.Stress),file=paste0("./analysis/",opt$g,"/global/DEG/DWS.scStress.txt"),sep="\n")