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3
|
1 require("ChIPseeker", quietly = TRUE)
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|
|
2 require("ChIPpeakAnno", quietly = TRUE)
|
|
|
3 require("EnsDb.Hsapiens.v75", quietly = TRUE)
|
|
5
|
4 require("data.table", quietly = TRUE)
|
|
3
|
5
|
|
0
|
6 options(warn = -1)
|
|
3
|
7 options("download.file.method"="wget")
|
|
0
|
8
|
|
|
9 args <- commandArgs(trailingOnly = TRUE)
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|
|
10 DMR = args[1]
|
|
4
|
11 annoPeakFigure = args[2]
|
|
0
|
12
|
|
5
|
13 DMRInfo = fread(
|
|
0
|
14 DMR,
|
|
|
15 header = FALSE,
|
|
|
16 sep = "\t",
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|
|
17 stringsAsFactors = FALSE,
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|
|
18 quote = ""
|
|
|
19 )
|
|
|
20
|
|
3
|
21 peaks <- GRanges(seqnames = DMRInfo[, 1],
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|
|
22 ranges = IRanges
|
|
|
23 (start = DMRInfo[, 2], end = DMRInfo[, 3]))
|
|
0
|
24
|
|
3
|
25 annoData <- toGRanges(EnsDb.Hsapiens.v75)
|
|
|
26 seqlevelsStyle(peaks) <- seqlevelsStyle(annoData)
|
|
0
|
27
|
|
5
|
28
|
|
3
|
29 anno <- annoPeaks(peaks, annoData=annoData,bindingType ="startSite")
|
|
0
|
30
|
|
3
|
31
|
|
|
32 png(file = annoPeakFigure,
|
|
1
|
33 width = 1200,
|
|
|
34 height = 600)
|
|
|
35
|
|
3
|
36 pie1(table(anno$insideFeature))
|
|
1
|
37
|
|
|
38 dev.off()
|
|
|
39
|
