From 85e676b1310f7eb1f8357568d86953959728221b Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Sat, 15 Aug 2020 22:53:27 -0500
Subject: [PATCH] Remove unnecessary columns on tpm table
---
workflow/scripts/convertGeneSymbols.R | 5 ++++-
1 file changed, 4 insertions(+), 1 deletion(-)
diff --git a/workflow/scripts/convertGeneSymbols.R b/workflow/scripts/convertGeneSymbols.R
index 7b05b92..452f450 100644
--- a/workflow/scripts/convertGeneSymbols.R
+++ b/workflow/scripts/convertGeneSymbols.R
@@ -10,6 +10,9 @@ rm(option_list)
countTable <- read.csv(paste0(opt$repRID,".countData.countTable.csv"), stringsAsFactors=FALSE)
geneID <- read.delim("geneID.tsv", header=FALSE, stringsAsFactors=FALSE)
Entrez <- read.delim("Entrez.tsv", header=FALSE, stringsAsFactors=FALSE)
+convert <- merge(x=Entrex,y=geneID,by.x="V1",by.y="V1",all.x=TRUE)
+
+
convert <- data.frame(geneID=countTable$Geneid)
convert <- merge(x=convert,y=geneID[,1:2],by.x="geneID",by.y="V2",all.x=TRUE)
@@ -21,4 +24,4 @@ convert <- unique(convert)
output <- merge(x=convert,y=countTable,by.x="GeneID",by.y="Geneid",all.x=TRUE)
-write.table(output,file=paste0(opt$repRID,".tpmTable.csv"),sep=",",row.names=FALSE,quote=FALSE)
\ No newline at end of file
+write.table(output,file=paste0(opt$repRID,".tpmTable.csv"),sep=",",row.names=FALSE,quote=FALSE)
--
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