Mercurial > repos > testtool > annotate_peak

comparison annotatePeak/annotatePeak.R @ 1:92387cb81962 draft

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author testtool
date Sat, 25 Feb 2017 11:18:27 -0500
parents 5d70366e7c6f
children be66730c5c3b
comparison
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0:5d70366e7c6f 1:92387cb81962
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 options(warn = -1) 4 options(warn = -1)
4 5
5 args <- commandArgs(trailingOnly = TRUE) 6 args <- commandArgs(trailingOnly = TRUE)
6 DMR = args[1] 7 DMR = args[1]
7 annoPeakTable = args[2] 8 annoPeakTable = args[2]
19 ranges = IRanges 20 ranges = IRanges
20 (start = DMRInfo[, 2], end = DMRInfo[, 3])) 21 (start = DMRInfo[, 2], end = DMRInfo[, 3]))
21 22
22 annotatePeak <- 23 annotatePeak <-
23 as.data.frame(annotatePeak(DMRPeaks, level = "gene", annoDb = "org.Hs.eg.db")) 24 as.data.frame(annotatePeak(DMRPeaks, level = "gene", annoDb = "org.Hs.eg.db"))
24 25 ??org.Hs.eg.db
25 26
26 write.csv(annotatePeak, annoPeakTable, row.names = FALSE) 27 write.csv(annotatePeak, annoPeakTable, row.names = FALSE)