Mercurial > repos > testtool > annotate_peak

changeset 13:77c0aee75ac6 draft

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Uploaded
author testtool
date Thu, 16 Mar 2017 07:28:01 -0400
parents 54e19bceff70
children 4a489b0d247f
files annotate_peak/._annotatePeak.R annotate_peak/annotatePeak.R
diffstat 2 files changed, 6 insertions(+), 4 deletions(-) [+]
line wrap: on
line diff
Binary file annotate_peak/._annotatePeak.R has changed
--- a/annotate_peak/annotatePeak.R	Thu Mar 16 07:21:37 2017 -0400
+++ b/annotate_peak/annotatePeak.R	Thu Mar 16 07:28:01 2017 -0400
@@ -1,14 +1,14 @@
 require("ChIPseeker", quietly = TRUE)
 require("ChIPpeakAnno", quietly = TRUE)
-require("org.Hs.eg.db", quietly = TRUE)
-require("GenomicRanges", quietly = TRUE)
+
 options(warn = -1)
+options("download.file.method"="wget")
 
 args <- commandArgs(trailingOnly = TRUE)
 DMR = args[1]
 annoPeakTable = args[2]
 
-
+DMR <- ("test-data/DMR.bed")
 DMRInfo = read.table(
   DMR,
   header = FALSE,
@@ -21,6 +21,8 @@
                     ranges = IRanges
                     (start = DMRInfo[, 2], end = DMRInfo[, 3]))
 
-annotatePeak <- as.data.frame(annotatePeak(DMRPeaks, level = "gene", annoDb = "org.Hs.eg.db"))
+annotatePeak <-
+  as.data.frame(annotatePeak(DMRPeaks, level = "gene", annoDb = "org.Hs.eg.db"))
 
+annoPeakTable <- ('test-data/annoPeakTable.csv')
 write.csv(annotatePeak, annoPeakTable, row.names = FALSE)