Mercurial > repos > testtool > annotate_peak

comparison annotate_peak/annotatePeak.R @ 18:6a9b9694acbf draft

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author testtool
date Mon, 20 Mar 2017 06:51:22 -0400
parents 982a01524118
children 741b192da59c
comparison
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17:982a01524118 18:6a9b9694acbf
1 require("ChIPseeker", quietly = TRUE) 1 require("ChIPseeker", quietly = TRUE)
2 require("ChIPpeakAnno", quietly = TRUE) 2 require("ChIPpeakAnno", quietly = TRUE)
3 require("EnsDb.Hsapiens.v75", quietly = TRUE) 3 require("EnsDb.Hsapiens.v75", quietly = TRUE)
4 require("data.table", quietly = TRUE)
4 5
5 options(warn = -1) 6 options(warn = -1)
6 options("download.file.method"="wget") 7 options("download.file.method"="wget")
7 8
8 args <- commandArgs(trailingOnly = TRUE) 9 args <- commandArgs(trailingOnly = TRUE)
9 DMR = args[1] 10 DMR = args[1]
10 annoPeakTable = args[2] 11 annoPeakTable = args[2]
11 12
12 #DMR <- ("test-data/DMR.bed") 13 DMRInfo = fread(
13 DMRInfo = read.table(
14 DMR, 14 DMR,
15 header = FALSE, 15 header = FALSE,
16 sep = "\t", 16 sep = "\t",
17 stringsAsFactors = FALSE, 17 stringsAsFactors = FALSE,
18 quote = "" 18 quote = ""
25 annoData <- toGRanges(EnsDb.Hsapiens.v75) 25 annoData <- toGRanges(EnsDb.Hsapiens.v75)
26 seqlevelsStyle(peaks) <- seqlevelsStyle(annoData) 26 seqlevelsStyle(peaks) <- seqlevelsStyle(annoData)
27 27
28 anno <- annoPeaks(peaks, annoData=annoData,bindingType ="startSite") 28 anno <- annoPeaks(peaks, annoData=annoData,bindingType ="startSite")
29 29
30 #annoPeakTable <- ('test-data/ChIPPeak.csv') 30 write.table(anno, annoPeakTable, row.names = FALSE)
31 write.csv(anno, annoPeakTable, row.names = FALSE)