Mercurial > repos > testtool > annotate_peak
view annotate_peak/annotatePeak.R @ 14:4a489b0d247f draft
Uploaded
author | testtool |
---|---|
date | Thu, 16 Mar 2017 10:59:08 -0400 |
parents | 77c0aee75ac6 |
children | 53df7871db21 |
line wrap: on
line source
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] ## try http:// if https:// URLs are not supported source("https://bioconductor.org/biocLite.R") biocLite("EnsDb.Hsapiens.v75") library(EnsDb.Hsapiens.v75) 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)