From cdd32cb3bce9534ffa93f12da14324acb0e2d11e Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Thu, 17 Dec 2020 15:53:46 -0600
Subject: [PATCH] Fix convert gene symbol script to use new countTable name
---
workflow/scripts/convertGeneSymbols.R | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/workflow/scripts/convertGeneSymbols.R b/workflow/scripts/convertGeneSymbols.R
index 49752f1..05a1528 100644
--- a/workflow/scripts/convertGeneSymbols.R
+++ b/workflow/scripts/convertGeneSymbols.R
@@ -7,7 +7,7 @@ option_list=list(
opt=parse_args(OptionParser(option_list=option_list))
rm(option_list)
-countTable <- read.csv(paste0(opt$repRID,".countTable.csv"), stringsAsFactors=FALSE)
+countTable <- read.csv(paste0(opt$repRID,"_countTable.csv"), stringsAsFactors=FALSE)
geneID <- read.delim("geneID.tsv", header=FALSE, stringsAsFactors=FALSE)
Entrez <- read.delim("Entrez.tsv", header=FALSE, stringsAsFactors=FALSE)
--
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