Mercurial > repos > testtool > annotate_peak

comparison annotate_peak/annotatePeak.R @ 19:741b192da59c draft

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author testtool
date Mon, 20 Mar 2017 07:19:42 -0400
parents 6a9b9694acbf
children 2044ad2c1c93
comparison
equal deleted inserted replaced
18:6a9b9694acbf 19:741b192da59c
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 require("EnsDb.Mmusculus.v75", quietly = TRUE)
5 5
6 options(warn = -1) 6 options(warn = -1)
7 options("download.file.method"="wget") 7 options("download.file.method"="wget")
8 8
9 args <- commandArgs(trailingOnly = TRUE) 9 args <- commandArgs(trailingOnly = TRUE)
10 DMR = args[1] 10 DMR = args[1]
11 annoPeakTable = args[2] 11 annoData = args[2]
12 bindingType = args[3]
13 upstream = as.numeric(args[4])
14 downstream = as.numeric(args[5])
15 ignore = args[6]
16 annoPeakTable = args[7]
12 17
13 DMRInfo = fread( 18 #DMR <- ("test-data/DMR.bed")
19 DMRInfo = read.table(
14 DMR, 20 DMR,
15 header = FALSE, 21 header = FALSE,
16 sep = "\t", 22 sep = "\t",
17 stringsAsFactors = FALSE, 23 stringsAsFactors = FALSE,
18 quote = "" 24 quote = ""
20 26
21 peaks <- GRanges(seqnames = DMRInfo[, 1], 27 peaks <- GRanges(seqnames = DMRInfo[, 1],
22 ranges = IRanges 28 ranges = IRanges
23 (start = DMRInfo[, 2], end = DMRInfo[, 3])) 29 (start = DMRInfo[, 2], end = DMRInfo[, 3]))
24 30
25 annoData <- toGRanges(EnsDb.Hsapiens.v75) 31
32 if (annoData == "human"){
33 annoData <- toGRanges(EnsDb.Hsapiens.v75)
34 } else {
35 annoData <- toGRanges(EnsDb.Mmusculus.v75)
36 }
26 seqlevelsStyle(peaks) <- seqlevelsStyle(annoData) 37 seqlevelsStyle(peaks) <- seqlevelsStyle(annoData)
27 38
28 anno <- annoPeaks(peaks, annoData=annoData,bindingType ="startSite") 39 if (ignore == "true"){
40 x <- TRUE
41 } else {
42 x <- FALSE
43 }
44
45
46 if (bindingType =="startSite"){
47 anno <- annoPeaks(peaks, annoData=annoData, bindingType =c("startSite"), bindingRegion=c(upstream, downstream), ignore.peak.strand = x)
48 } else if (bindingType =="endSite"){
49 anno <- annoPeaks(peaks, annoData=annoData, bindingType =c("endSite"), bindingRegion=c(upstream, downstream), ignore.peak.strand = x)
50 } else {
51 anno <- annoPeaks(peaks, annoData=annoData, bindingType =c("fullRange"), bindingRegion=c(upstream, downstream), ignore.peak.strand = x)
52 }
53
29 54
30 write.table(anno, annoPeakTable, row.names = FALSE) 55 write.table(anno, annoPeakTable, row.names = FALSE)