Mercurial > repos > kpbioteam > chipeakanno_annopeaks

comparison chipeakanno_annopeaks.R @ 1:a90b6d85463c draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/kpbioteam/chipeakanno_annopeaks commit b7298370ebae64340e792262c4e4f35568757871-dirty
author kpbioteam
date Wed, 02 May 2018 10:23:51 -0400
parents efd9e1315ed5
children 9ec5e9e2e7b2
comparison
equal deleted inserted replaced
0:efd9e1315ed5 1:a90b6d85463c
11 input2 = args[2] 11 input2 = args[2]
12 input3 = as.numeric(args[3]) 12 input3 = as.numeric(args[3])
13 input4 = as.numeric(args[4]) 13 input4 = as.numeric(args[4])
14 output1 = args[5] 14 output1 = args[5]
15 15
16 peaks <- get(load(input1)) 16 DMRInfo <- read.table(input1)
17 peaks <- GRanges(seqnames = DMRInfo[, 1],
18 ranges = IRanges
19 (start = DMRInfo[, 2], end = DMRInfo[, 3]))
17 20
18 annoData <- toGRanges(EnsDb.Hsapiens.v75) 21 annoData <- toGRanges(EnsDb.Hsapiens.v75)
19 seqlevelsStyle(peaks) <- seqlevelsStyle(annoData) 22 seqlevelsStyle(peaks) <- seqlevelsStyle(annoData)
20 23
21 anno <- annoPeaks(peaks, annoData=annoData, bindingType =c(input2), bindingRegion=c(input3, input4)) 24 anno <- annoPeaks(peaks, annoData=annoData, bindingType =c(input2), bindingRegion=c(input3, input4))