Mercurial > repos > testtool > annotate_peak

comparison annotate_peak/annotatePeak.R @ 17:982a01524118 draft

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author testtool
date Thu, 16 Mar 2017 16:13:45 -0400
parents ee3fc24b2108
children 6a9b9694acbf
comparison
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16:ee3fc24b2108 17:982a01524118
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("GenomicRanges", quietly = TRUE)
5 4
6 options(warn = -1) 5 options(warn = -1)
6 options("download.file.method"="wget")
7
7 args <- commandArgs(trailingOnly = TRUE) 8 args <- commandArgs(trailingOnly = TRUE)
8 DMR = args[1] 9 DMR = args[1]
9 annoPeakTable = args[2] 10 annoPeakTable = args[2]
10 11
11 #DMR <- ("test-data/DMR.bed") 12 #DMR <- ("test-data/DMR.bed")
18 ) 19 )
19 20
20 peaks <- GRanges(seqnames = DMRInfo[, 1], 21 peaks <- GRanges(seqnames = DMRInfo[, 1],
21 ranges = IRanges 22 ranges = IRanges
22 (start = DMRInfo[, 2], end = DMRInfo[, 3])) 23 (start = DMRInfo[, 2], end = DMRInfo[, 3]))
23 peaks[1:2] 24
24 annoData <- toGRanges(EnsDb.Hsapiens.v75) 25 annoData <- toGRanges(EnsDb.Hsapiens.v75)
25 annoData[1:2] 26 seqlevelsStyle(peaks) <- seqlevelsStyle(annoData)
26 27
27 ## keep the seqnames in the same style 28 anno <- annoPeaks(peaks, annoData=annoData,bindingType ="startSite")
28 seqlevelsStyle(peaks) <- seqlevelsStyle(annoData) 29
29 ## do annotation by nearest TSS
30 anno <- annotatePeakInBatch(peaks, AnnotationData=annoData)
31 anno[1:2]
32 #annoPeakTable <- ('test-data/ChIPPeak.csv') 30 #annoPeakTable <- ('test-data/ChIPPeak.csv')
33 write.csv(anno, annoPeakTable, row.names = FALSE) 31 write.csv(anno, annoPeakTable, row.names = FALSE)
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