Mercurial > repos > testtool > annotate_peak

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

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author testtool
date Thu, 16 Mar 2017 07:28:01 -0400
parents 54e19bceff70
children 4a489b0d247f
comparison
equal deleted inserted replaced
12:54e19bceff70 13:77c0aee75ac6
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
4 require("GenomicRanges", quietly = TRUE)
5 options(warn = -1) 4 options(warn = -1)
5 options("download.file.method"="wget")
6 6
7 args <- commandArgs(trailingOnly = TRUE) 7 args <- commandArgs(trailingOnly = TRUE)
8 DMR = args[1] 8 DMR = args[1]
9 annoPeakTable = args[2] 9 annoPeakTable = args[2]
10 10
11 11 DMR <- ("test-data/DMR.bed")
12 DMRInfo = read.table( 12 DMRInfo = read.table(
13 DMR, 13 DMR,
14 header = FALSE, 14 header = FALSE,
15 sep = "\t", 15 sep = "\t",
16 stringsAsFactors = FALSE, 16 stringsAsFactors = FALSE,
19 19
20 DMRPeaks <- GRanges(seqnames = DMRInfo[, 1], 20 DMRPeaks <- GRanges(seqnames = DMRInfo[, 1],
21 ranges = IRanges 21 ranges = IRanges
22 (start = DMRInfo[, 2], end = DMRInfo[, 3])) 22 (start = DMRInfo[, 2], end = DMRInfo[, 3]))
23 23
24 annotatePeak <- as.data.frame(annotatePeak(DMRPeaks, level = "gene", annoDb = "org.Hs.eg.db")) 24 annotatePeak <-
25 as.data.frame(annotatePeak(DMRPeaks, level = "gene", annoDb = "org.Hs.eg.db"))
25 26
27 annoPeakTable <- ('test-data/annoPeakTable.csv')
26 write.csv(annotatePeak, annoPeakTable, row.names = FALSE) 28 write.csv(annotatePeak, annoPeakTable, row.names = FALSE)