Mercurial > repos > testtool > annotate_peak
comparison annotate_peak/annotatePeak.R @ 15:53df7871db21 draft
Uploaded
author | testtool |
---|---|
date | Thu, 16 Mar 2017 11:03:24 -0400 |
parents | 4a489b0d247f |
children | ee3fc24b2108 |
comparison
equal
deleted
inserted
replaced
14:4a489b0d247f | 15:53df7871db21 |
---|---|
1 options(warn = -1) | 1 options(warn = -1) |
2 args <- commandArgs(trailingOnly = TRUE) | 2 args <- commandArgs(trailingOnly = TRUE) |
3 DMR = args[1] | 3 DMR = args[1] |
4 annoPeakTable = args[2] | 4 annoPeakTable = args[2] |
5 | 5 |
6 DMR <- ("test-data/DMR.bed") | 6 #DMR <- ("test-data/DMR.bed") |
7 DMRInfo = read.table( | 7 DMRInfo = read.table( |
8 DMR, | 8 DMR, |
9 header = FALSE, | 9 header = FALSE, |
10 sep = "\t", | 10 sep = "\t", |
11 stringsAsFactors = FALSE, | 11 stringsAsFactors = FALSE, |
26 ## keep the seqnames in the same style | 26 ## keep the seqnames in the same style |
27 seqlevelsStyle(peaks) <- seqlevelsStyle(annoData) | 27 seqlevelsStyle(peaks) <- seqlevelsStyle(annoData) |
28 ## do annotation by nearest TSS | 28 ## do annotation by nearest TSS |
29 anno <- annotatePeakInBatch(peaks, AnnotationData=annoData) | 29 anno <- annotatePeakInBatch(peaks, AnnotationData=annoData) |
30 anno[1:2] | 30 anno[1:2] |
31 annoPeakTable <- ('test-data/ChIPPeak.csv') | 31 #annoPeakTable <- ('test-data/ChIPPeak.csv') |
32 write.csv(anno, annoPeakTable, row.names = FALSE) | 32 write.csv(anno, annoPeakTable, row.names = FALSE) |
33 | 33 |
34 | 34 |