Mercurial > repos > testtool > annotate_peak
comparison annotate_peak/annotatePeak.R @ 18:6a9b9694acbf draft
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author | testtool |
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date | Mon, 20 Mar 2017 06:51:22 -0400 |
parents | 982a01524118 |
children | 741b192da59c |
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17:982a01524118 | 18:6a9b9694acbf |
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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) |