diff annotatePeak/.Rhistory @ 3:7beb1a8f7cb0 draft

Uploaded

--- 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"))