Mercurial > repos > testtool > annotate_peak
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(-) [+] |
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--- 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)