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view annotate_peak/annotatePeak.R @ 13:77c0aee75ac6 draft

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author testtool
date Thu, 16 Mar 2017 07:28:01 -0400
parents 54e19bceff70
children 4a489b0d247f
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require("ChIPseeker", quietly = TRUE)
require("ChIPpeakAnno", 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 = ""
)

DMRPeaks <- GRanges(seqnames = DMRInfo[, 1],
                    ranges = IRanges
                    (start = DMRInfo[, 2], end = DMRInfo[, 3]))

annotatePeak <-
  as.data.frame(annotatePeak(DMRPeaks, level = "gene", annoDb = "org.Hs.eg.db"))

annoPeakTable <- ('test-data/annoPeakTable.csv')
write.csv(annotatePeak, annoPeakTable, row.names = FALSE)