From e7b72cfb4b5adae63053a7c256834c1b34b59a35 Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Wed, 26 Dec 2018 19:23:34 -0600
Subject: [PATCH] Change R version and output.
---
workflow/conf/biohpc.config | 2 +-
workflow/scripts/annotate_peaks.R | 14 +++++---------
2 files changed, 6 insertions(+), 10 deletions(-)
diff --git a/workflow/conf/biohpc.config b/workflow/conf/biohpc.config
index c6d3953..6c9806f 100644
--- a/workflow/conf/biohpc.config
+++ b/workflow/conf/biohpc.config
@@ -49,7 +49,7 @@ process {
executor = 'local'
}
withName: peakAnnotation {
- module = ['R/3.4.1-gccmkl']
+ module = ['R/3.3.2-gccmkl']
executor = 'local'
}
withName: diffPeaks {
diff --git a/workflow/scripts/annotate_peaks.R b/workflow/scripts/annotate_peaks.R
index 63fa051..3661bc0 100644
--- a/workflow/scripts/annotate_peaks.R
+++ b/workflow/scripts/annotate_peaks.R
@@ -8,11 +8,8 @@ library("ChIPseeker")
library("TxDb.Hsapiens.UCSC.hg19.knownGene")
library("TxDb.Mmusculus.UCSC.mm10.knownGene")
library("TxDb.Hsapiens.UCSC.hg38.knownGene")
-
-source("http://bioconductor.org/biocLite.R")
-if(!require("ChIPseeker")){
- biocLite("ChIPseeker")
-}
+library("org.Hs.eg.db")
+library("org.Mm.eg.db")
# Create parser object
@@ -29,13 +26,13 @@ genome <-args[2]
# Load UCSC Known Genes
if(genome=='GRCh37') {
txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
- annodb <- org.Hs.eg.db
+ annodb <- 'org.Hs.eg.db'
} else if(genome=='GRCm38') {
txdb <- TxDb.Mmusculus.UCSC.mm10.knownGene
- annodb <- org.Mm.eg.db
+ annodb <- 'org.Mm.eg.db'
} else if(genome=='GRCh38') {
txdb <- TxDb.Hsapiens.UCSC.hg38.knownGene
- annodb <- org.Hs.eg.db
+ annodb <- 'org.Hs.eg.db'
}
# Load design file
@@ -45,7 +42,6 @@ names(files) <- design$Condition
peakAnnoList <- lapply(files, annotatePeak, TxDb=txdb, annoDb=annodb, tssRegion=c(-3000, 3000), verbose=FALSE)
-
for(index in c(1:length(peakAnnoList))) {
filename <- paste(names(files)[index],".chipseeker_annotation.csv",sep="")
write.table(as.data.frame(peakAnnoList[[index]]),filename,sep=",",quote=F)
--
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