Mercurial > repos > testtool > annotate_peak

changeset 2:be66730c5c3b draft

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Uploaded
author testtool
date Sat, 25 Feb 2017 11:29:01 -0500
parents 92387cb81962
children 7beb1a8f7cb0
files annotatePeak/annotatePeak.R
diffstat 1 files changed, 4 insertions(+), 4 deletions(-) [+]
line wrap: on
line diff
--- a/annotatePeak/annotatePeak.R	Sat Feb 25 11:18:27 2017 -0500
+++ b/annotatePeak/annotatePeak.R	Sat Feb 25 11:29:01 2017 -0500
@@ -1,6 +1,7 @@
 require("ChIPseeker", quietly = TRUE)
 require("ChIPpeakAnno", quietly = TRUE)
 require("org.Hs.eg.db", quietly = TRUE)
+require("GenomicRanges", quietly = TRUE)
 options(warn = -1)
 
 args <- commandArgs(trailingOnly = TRUE)
@@ -20,8 +21,7 @@
                     ranges = IRanges
                     (start = DMRInfo[, 2], end = DMRInfo[, 3]))
 
-annotatePeak <-
-  as.data.frame(annotatePeak(DMRPeaks, level = "gene", annoDb = "org.Hs.eg.db"))
-??org.Hs.eg.db
+annotatePeak <- annotatePeak(DMRPeaks, level = "gene", annoDb = "org.Hs.eg.db")
 
-write.csv(annotatePeak, annoPeakTable, row.names = FALSE)
+
+write.csv(as.data.frame(annotatePeak), annoPeakTable, row.names = FALSE)