Mercurial > repos > kpbioteam > chipeakanno_annopeaks
comparison chipeakanno_annopeaks.R @ 0:efd9e1315ed5 draft
planemo upload for repository https://github.com/kpbioteam/chipeakanno_annopeaks commit b81bbf4662bc9f8a936ccdf5813c3cd8020c579d-dirty
| author | kpbioteam |
|---|---|
| date | Wed, 02 May 2018 09:24:03 -0400 |
| parents | |
| children | a90b6d85463c |
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| -1:000000000000 | 0:efd9e1315ed5 |
|---|---|
| 1 require("ChIPpeakAnno", quietly = TRUE) | |
| 2 require("EnsDb.Hsapiens.v75", quietly = TRUE) | |
| 3 require("rtracklayer", quietly = TRUE) | |
| 4 | |
| 5 options(warn = -1) | |
| 6 options("download.file.method"="wget") | |
| 7 | |
| 8 args <- commandArgs(trailingOnly = TRUE) | |
| 9 | |
| 10 input1 = args[1] | |
| 11 input2 = args[2] | |
| 12 input3 = as.numeric(args[3]) | |
| 13 input4 = as.numeric(args[4]) | |
| 14 output1 = args[5] | |
| 15 | |
| 16 peaks <- get(load(input1)) | |
| 17 | |
| 18 annoData <- toGRanges(EnsDb.Hsapiens.v75) | |
| 19 seqlevelsStyle(peaks) <- seqlevelsStyle(annoData) | |
| 20 | |
| 21 anno <- annoPeaks(peaks, annoData=annoData, bindingType =c(input2), bindingRegion=c(input3, input4)) | |
| 22 | |
| 23 write.table(anno, file= output1, row.names = FALSE) |