changeset 1:92387cb81962 draft

Uploaded
author testtool
date Sat, 25 Feb 2017 11:18:27 -0500
parents 5d70366e7c6f
children be66730c5c3b
files annotatePeak/.Rhistory annotatePeak/annotatePeak.R
diffstat 2 files changed, 19 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- a/annotatePeak/.Rhistory	Mon Feb 06 10:53:57 2017 -0500
+++ b/annotatePeak/.Rhistory	Sat Feb 25 11:18:27 2017 -0500
@@ -154,3 +154,20 @@
 dev.off()
 png(figure)
 upsetplot(anno, vennpie=TRUE)
+org.Hs.eg.db
+??org.Hs.eg.db
+require("ChIPseeker", quietly = TRUE)
+require("ChIPpeakAnno", quietly = TRUE)
+DMRInfo = read.table(
+DMR,
+header = FALSE,
+sep = "\t",
+stringsAsFactors = FALSE,
+quote = ""
+)
+DMRPeaks <- GRanges(seqnames = DMRInfo[, 1],
+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
--- a/annotatePeak/annotatePeak.R	Mon Feb 06 10:53:57 2017 -0500
+++ b/annotatePeak/annotatePeak.R	Sat Feb 25 11:18:27 2017 -0500
@@ -1,5 +1,6 @@
 require("ChIPseeker", quietly = TRUE)
 require("ChIPpeakAnno", quietly = TRUE)
+require("org.Hs.eg.db", quietly = TRUE)
 options(warn = -1)
 
 args <- commandArgs(trailingOnly = TRUE)
@@ -21,6 +22,6 @@
 
 annotatePeak <-
   as.data.frame(annotatePeak(DMRPeaks, level = "gene", annoDb = "org.Hs.eg.db"))
-
+??org.Hs.eg.db
 
 write.csv(annotatePeak, annoPeakTable, row.names = FALSE)