Mercurial > repos > testtool > annotate_peak

comparison annotatePeak/annotatePeak.R @ 2:be66730c5c3b draft

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author testtool
date Sat, 25 Feb 2017 11:29:01 -0500
parents 92387cb81962
children e1c643f600d2
comparison
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1:92387cb81962 2:be66730c5c3b
1 require("ChIPseeker", quietly = TRUE) 1 require("ChIPseeker", quietly = TRUE)
2 require("ChIPpeakAnno", quietly = TRUE) 2 require("ChIPpeakAnno", quietly = TRUE)
3 require("org.Hs.eg.db", quietly = TRUE) 3 require("org.Hs.eg.db", quietly = TRUE)
4 require("GenomicRanges", quietly = TRUE)
4 options(warn = -1) 5 options(warn = -1)
5 6
6 args <- commandArgs(trailingOnly = TRUE) 7 args <- commandArgs(trailingOnly = TRUE)
7 DMR = args[1] 8 DMR = args[1]
8 annoPeakTable = args[2] 9 annoPeakTable = args[2]
18 19
19 DMRPeaks <- GRanges(seqnames = DMRInfo[, 1], 20 DMRPeaks <- GRanges(seqnames = DMRInfo[, 1],
20 ranges = IRanges 21 ranges = IRanges
21 (start = DMRInfo[, 2], end = DMRInfo[, 3])) 22 (start = DMRInfo[, 2], end = DMRInfo[, 3]))
22 23
23 annotatePeak <- 24 annotatePeak <- annotatePeak(DMRPeaks, level = "gene", annoDb = "org.Hs.eg.db")
24 as.data.frame(annotatePeak(DMRPeaks, level = "gene", annoDb = "org.Hs.eg.db"))
25 ??org.Hs.eg.db
26 25
27 write.csv(annotatePeak, annoPeakTable, row.names = FALSE) 26
27 write.csv(as.data.frame(annotatePeak), annoPeakTable, row.names = FALSE)