Mercurial > repos > testtool > annotate_peak

comparison annotate_peak/annotatePeak.R @ 16:ee3fc24b2108 draft

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author testtool
date Thu, 16 Mar 2017 11:23:38 -0400
parents 53df7871db21
children 982a01524118
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15:53df7871db21 16:ee3fc24b2108
1 require("ChIPseeker", quietly = TRUE)
2 require("ChIPpeakAnno", quietly = TRUE)
3 require("EnsDb.Hsapiens.v75", quietly = TRUE)
4 require("GenomicRanges", quietly = TRUE)
5
1 options(warn = -1) 6 options(warn = -1)
2 args <- commandArgs(trailingOnly = TRUE) 7 args <- commandArgs(trailingOnly = TRUE)
3 DMR = args[1] 8 DMR = args[1]
4 annoPeakTable = args[2] 9 annoPeakTable = args[2]
5 10
14 19
15 peaks <- GRanges(seqnames = DMRInfo[, 1], 20 peaks <- GRanges(seqnames = DMRInfo[, 1],
16 ranges = IRanges 21 ranges = IRanges
17 (start = DMRInfo[, 2], end = DMRInfo[, 3])) 22 (start = DMRInfo[, 2], end = DMRInfo[, 3]))
18 peaks[1:2] 23 peaks[1:2]
19 ## try http:// if https:// URLs are not supported
20 source("https://bioconductor.org/biocLite.R")
21 biocLite("EnsDb.Hsapiens.v75")
22 library(EnsDb.Hsapiens.v75)
23 annoData <- toGRanges(EnsDb.Hsapiens.v75) 24 annoData <- toGRanges(EnsDb.Hsapiens.v75)
24 annoData[1:2] 25 annoData[1:2]
25 26
26 ## keep the seqnames in the same style 27 ## keep the seqnames in the same style
27 seqlevelsStyle(peaks) <- seqlevelsStyle(annoData) 28 seqlevelsStyle(peaks) <- seqlevelsStyle(annoData)