# HG changeset patch
# User testtool
# Date 1489663681 14400
# Node ID 77c0aee75ac6e867ea35574d0e711d3ec74d41fb
# Parent  54e19bceff70339af670a11c41645b523180e491
Uploaded

diff -r 54e19bceff70 -r 77c0aee75ac6 annotate_peak/._annotatePeak.R
Binary file annotate_peak/._annotatePeak.R has changed
diff -r 54e19bceff70 -r 77c0aee75ac6 annotate_peak/annotatePeak.R
--- 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)