Mercurial > repos > testtool > annotate_peak
view annotate_peak/annotatePeak.R @ 17:982a01524118 draft
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author | testtool |
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date | Thu, 16 Mar 2017 16:13:45 -0400 |
parents | ee3fc24b2108 |
children | 6a9b9694acbf |
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require("ChIPseeker", quietly = TRUE) require("ChIPpeakAnno", quietly = TRUE) require("EnsDb.Hsapiens.v75", quietly = TRUE) options(warn = -1) options("download.file.method"="wget") args <- commandArgs(trailingOnly = TRUE) DMR = args[1] annoPeakTable = args[2] #DMR <- ("test-data/DMR.bed") DMRInfo = read.table( DMR, header = FALSE, sep = "\t", stringsAsFactors = FALSE, quote = "" ) peaks <- GRanges(seqnames = DMRInfo[, 1], ranges = IRanges (start = DMRInfo[, 2], end = DMRInfo[, 3])) annoData <- toGRanges(EnsDb.Hsapiens.v75) seqlevelsStyle(peaks) <- seqlevelsStyle(annoData) anno <- annoPeaks(peaks, annoData=annoData,bindingType ="startSite") #annoPeakTable <- ('test-data/ChIPPeak.csv') write.csv(anno, annoPeakTable, row.names = FALSE)