From 1f1c60757541e7fa711f90f2232267ff85429d94 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Fri, 6 Mar 2020 17:11:59 -0600
Subject: [PATCH] Remove edgeR from calculateTPM script
---
workflow/scripts/calcuateTPM.R | 3 +--
1 file changed, 1 insertion(+), 2 deletions(-)
diff --git a/workflow/scripts/calcuateTPM.R b/workflow/scripts/calcuateTPM.R
index 9451165..3643073 100644
--- a/workflow/scripts/calcuateTPM.R
+++ b/workflow/scripts/calcuateTPM.R
@@ -1,6 +1,5 @@
gc()
library(optparse)
-library(edgeR)
option_list=list(
make_option("--count",action="store",type='character',help="Count File")
@@ -29,4 +28,4 @@ tpm <- rpk/scale
output <- cbind(count,tpm)
colnames(output)[7] <- "count"
-write.table(output,file=paste0(repRID,".countTable.csv"),sep=",",row.names=FALSE,quote=FALSE)
\ No newline at end of file
+write.table(output,file=paste0(repRID,".countTable.csv"),sep=",",row.names=FALSE,quote=FALSE)
--
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