diff annotate_peak/.Rhistory @ 18:6a9b9694acbf draft

Uploaded

--- a/annotate_peak/.Rhistory	Thu Mar 16 16:13:45 2017 -0400
+++ b/annotate_peak/.Rhistory	Mon Mar 20 06:51:22 2017 -0400
@@ -136,3 +136,69 @@
 TAB = read.csv(csv_file)
 TAB
 ??bumphunter
+??toGranges
+require("ChIPseeker", quietly = TRUE)
+require("ChIPpeakAnno", quietly = TRUE)
+options(warn = -1)
+args <- commandArgs(trailingOnly = TRUE)
+DMR = args[1]
+annoPeakTable = args[2]
+DMRInfo = read.table(
+DMR,
+header = FALSE,
+sep = "\t",
+stringsAsFactors = FALSE,
+quote = ""
+)
+peaks <- GRanges(seqnames = DMRInfo[, 1],
+ranges = IRanges
+(start = DMRInfo[, 2], end = DMRInfo[, 3]))
+peaks[1:2]
+DMR <- ("test-data/DMR.bed")
+DMRInfo = read.table(
+DMR,
+header = FALSE,
+sep = "\t",
+stringsAsFactors = FALSE,
+quote = ""
+)
+peaks <- GRanges(seqnames = DMRInfo[, 1],
+ranges = IRanges
+(start = DMRInfo[, 2], end = DMRInfo[, 3]))
+source("https://bioconductor.org/biocLite.R")
+biocLite("EnsDb.Hsapiens.v75")
+peaks <- toGRanges(seqnames = DMRInfo[, 1],
+ranges = IRanges
+(start = DMRInfo[, 2], end = DMRInfo[, 3]))
+peaks <- toGRanges(DMRInfo)
+peaks <- toGRanges(seqnames = DMRInfo[, 1],
+ranges = IRanges
+(start = DMRInfo[, 2], end = DMRInfo[, 3]))
+DMR <- ("test-data/DMR.bed")
+DMRInfo = read.table(
+DMR,
+header = FALSE,
+sep = "\t",
+stringsAsFactors = FALSE,
+quote = ""
+)
+peaks <- toGRanges(seqnames = DMRInfo[, 1],
+ranges = IRanges
+(start = DMRInfo[, 2], end = DMRInfo[, 3]))
+peaks <- toGRanges(seqnames = DMRInfo[, 1], format=c("BED"), feature=c("gene"), header=FALSE,
+(start = DMRInfo[, 2], end = DMRInfo[, 3]))
+peaks <- toGRanges(seqnames = DMRInfo[, 1], format=c("BED")
+feature=c("gene") header=FALSE,(start = DMRInfo[, 2], end = DMRInfo[, 3]))
+peaks <- toGRanges(seqnames = DMRInfo[, 1], format=c("BED"(start = DMRInfo[, 2], end = DMRInfo[, 3]))
+peaks <- toGRanges(seqnames = DMRInfo[, 1], format=c("BED"(start = DMRInfo[, 2], end = DMRInfo[, 3]))
+class(DMRInfo)
+toGRanges(DMRInfo, seqnames = DMRInfo[, 1],(start = DMRInfo[, 2], end = DMRInfo[, 3]))
+toGRanges(DMRInfo, seqnames = DMRInfo[, 1],(start = DMRInfo[, 2] end = DMRInfo[, 3]))
+toGRanges(DMRInfo, seqnames = DMRInfo[, 1],start = DMRInfo[, 2], end = DMRInfo[, 3])
+toGRanges(DMRInfo, seqnames = DMRInfo[, 1](start = DMRInfo[, 2], end = DMRInfo[, 3]))
+toGRanges(DMRInfo, colNames = DMRInfo[, 1](start = DMRInfo[, 2], end = DMRInfo[, 3]))
+peaks <- toGRanges(DMRInfo)
+peaks <- GRanges(seqnames = DMRInfo[, 1],
+ranges = IRanges
+(start = DMRInfo[, 2], end = DMRInfo[, 3]))
+??fread