Mercurial > repos > testtool > annotate_peak
diff annotate_peak/annotatePeak.R @ 18:6a9b9694acbf draft
Uploaded
author | testtool |
---|---|
date | Mon, 20 Mar 2017 06:51:22 -0400 |
parents | 982a01524118 |
children | 741b192da59c |
line wrap: on
line diff
--- a/annotate_peak/annotatePeak.R Thu Mar 16 16:13:45 2017 -0400 +++ b/annotate_peak/annotatePeak.R Mon Mar 20 06:51:22 2017 -0400 @@ -1,6 +1,7 @@ require("ChIPseeker", quietly = TRUE) require("ChIPpeakAnno", quietly = TRUE) require("EnsDb.Hsapiens.v75", quietly = TRUE) +require("data.table", quietly = TRUE) options(warn = -1) options("download.file.method"="wget") @@ -9,8 +10,7 @@ DMR = args[1] annoPeakTable = args[2] -#DMR <- ("test-data/DMR.bed") -DMRInfo = read.table( +DMRInfo = fread( DMR, header = FALSE, sep = "\t", @@ -27,5 +27,4 @@ anno <- annoPeaks(peaks, annoData=annoData,bindingType ="startSite") -#annoPeakTable <- ('test-data/ChIPPeak.csv') -write.csv(anno, annoPeakTable, row.names = FALSE) \ No newline at end of file +write.table(anno, annoPeakTable, row.names = FALSE) \ No newline at end of file