Mercurial > repos > testtool > annotate_peak
diff annotatePeak/.Rhistory @ 3:7beb1a8f7cb0 draft
Uploaded
author | testtool |
---|---|
date | Mon, 27 Feb 2017 08:34:24 -0500 |
parents | 92387cb81962 |
children | e1c643f600d2 |
line wrap: on
line diff
--- a/annotatePeak/.Rhistory Sat Feb 25 11:29:01 2017 -0500 +++ b/annotatePeak/.Rhistory Mon Feb 27 08:34:24 2017 -0500 @@ -171,3 +171,60 @@ annotatePeak <- as.data.frame(annotatePeak(DMRPeaks, level = "gene", annoDb = "org.Hs.eg.db")) ??org.Hs.eg.db +DMR <- ("test-data/DMR.bed") +DMRInfo = read.table( +DMR, +header = FALSE, +sep = "\t", +stringsAsFactors = FALSE, +quote = "" +) +DMRPeaks <- GRanges(seqnames = DMRInfo[, 1], +ranges = IRanges +(start = DMRInfo[, 2], end = DMRInfo[, 3])) +??GRanges +require("GenomicRanges", quietly = TRUE) +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")) +require("ChIPseeker", quietly = TRUE) +require("ChIPpeakAnno", quietly = TRUE) +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")) +write.csv(as.data.frame(annotatePeak), annoPeakTable, row.names = FALSE) +DMR <- ("test-data/DMR.bed") +DMRInfo = read.table( +DMR, +header = FALSE, +sep = "\t", +stringsAsFactors = FALSE, +quote = "" +) +DMRPeaks <- GRanges(seqnames = DMRInfo[, 1], +ranges = IRanges +DMRPeaks <- GRanges(seqnames = DMRInfo[, 1], +ranges = IRanges +(start = DMRInfo[, 2], end = DMRInfo[, 3])) +??GRanges +options(warn = -1) +args <- commandArgs(trailingOnly = TRUE) +DMR = args[1] +annoPeakTable = args[2] +DMR <- ("test-data/DMR.bed") +DMRInfo = read.table( +DMR, +header = FALSE, +sep = "\t", +stringsAsFactors = FALSE, +quote = "" +) +DMRPeaks <- GRanges(seqnames = DMRInfo[, 1], +ranges = IRanges +(start = DMRInfo[, 2], end = DMRInfo[, 3])) +??GRanges +annotatePeak <- +as.data.frame(annotatePeak(DMRPeaks, level = "gene", annoDb = "org.Hs.eg.db"))