From 931b908608ba473fc21512e2ac327d3c92712c6b Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Tue, 25 Dec 2018 06:07:43 -0600
Subject: [PATCH] Termite annodb
---
workflow/scripts/annotate_peaks.R | 9 +--------
1 file changed, 1 insertion(+), 8 deletions(-)
diff --git a/workflow/scripts/annotate_peaks.R b/workflow/scripts/annotate_peaks.R
index 64d608d..2499757 100644
--- a/workflow/scripts/annotate_peaks.R
+++ b/workflow/scripts/annotate_peaks.R
@@ -10,10 +10,6 @@ library("TxDb.Mmusculus.UCSC.mm10.knownGene")
library("TxDb.Hsapiens.UCSC.hg38.knownGene")
-library("org.Hs.eg.db")
-library("org.Mm.eg.db")
-
-
# Create parser object
args <- commandArgs(trailingOnly=TRUE)
@@ -29,13 +25,10 @@ genome <-args[2]
# Load UCSC Known Genes
if(genome=='GRCh37') {
txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
- annodb <- org.Hs.eg.db
} else if(genome=='GRCm38') {
txdb <- TxDb.Mmusculus.UCSC.mm10.knownGene
- annodb <- org.Mm.eg.db
} else if(genome=='GRCh38') {
txdb <- TxDb.Hsapiens.UCSC.hg38.knownGene
- annodb <- org.Hs.eg.db
}
# Load design file
@@ -44,7 +37,7 @@ files <- as.list(as.character(design$Peaks))
names(files) <- design$Condition
-peakAnnoList <- lapply(files, annotatePeak, TxDb=txdb, annoDb=annodb, tssRegion=c(-3000, 3000), verbose=FALSE)
+peakAnnoList <- lapply(files, annotatePeak, TxDb=txdb, tssRegion=c(-3000, 3000), verbose=FALSE)
for(index in c(1:length(peakAnnoList))) {
filename <- paste(names(files)[index],".chipseeker_annotation.csv",sep="")
--
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