diff --git a/workflow/scripts/annotate_peaks.R b/workflow/scripts/annotate_peaks.R index 64d608d6574ce819ae8e9a88b20d4bc2d0770f00..2499757e5bcc8fbb76657cf49aac2d863f77cbb8 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="")