Mercurial > repos > testtool > annotate_peak
view annotate_peak/annotatePeak.R @ 16:ee3fc24b2108 draft
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author | testtool |
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date | Thu, 16 Mar 2017 11:23:38 -0400 |
parents | 53df7871db21 |
children | 982a01524118 |
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require("ChIPseeker", quietly = TRUE) require("ChIPpeakAnno", quietly = TRUE) require("EnsDb.Hsapiens.v75", quietly = TRUE) require("GenomicRanges", quietly = TRUE) options(warn = -1) 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])) peaks[1:2] annoData <- toGRanges(EnsDb.Hsapiens.v75) annoData[1:2] ## keep the seqnames in the same style seqlevelsStyle(peaks) <- seqlevelsStyle(annoData) ## do annotation by nearest TSS anno <- annotatePeakInBatch(peaks, AnnotationData=annoData) anno[1:2] #annoPeakTable <- ('test-data/ChIPPeak.csv') write.csv(anno, annoPeakTable, row.names = FALSE)