# HG changeset patch
# User testtool
# Date 1490007082 14400
# Node ID 6a9b9694acbf12080bb9202cab703476f8a61525
# Parent 982a0152411884f8a5b1e6503674eedf67cb77e5
Uploaded
diff -r 982a01524118 -r 6a9b9694acbf annotate_peak/.RData
Binary file annotate_peak/.RData has changed
diff -r 982a01524118 -r 6a9b9694acbf annotate_peak/.Rhistory
--- 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
diff -r 982a01524118 -r 6a9b9694acbf annotate_peak/annotatePeak.R
--- a/annotate_peak/annotatePeak.R Thu Mar 16 16:13:45 2017 -0400
+++ b/annotate_peak/annotatePeak.R Mon Mar 20 06:51:22 2017 -0400
@@ -1,6 +1,7 @@
require("ChIPseeker", quietly = TRUE)
require("ChIPpeakAnno", quietly = TRUE)
require("EnsDb.Hsapiens.v75", quietly = TRUE)
+require("data.table", quietly = TRUE)
options(warn = -1)
options("download.file.method"="wget")
@@ -9,8 +10,7 @@
DMR = args[1]
annoPeakTable = args[2]
-#DMR <- ("test-data/DMR.bed")
-DMRInfo = read.table(
+DMRInfo = fread(
DMR,
header = FALSE,
sep = "\t",
@@ -27,5 +27,4 @@
anno <- annoPeaks(peaks, annoData=annoData,bindingType ="startSite")
-#annoPeakTable <- ('test-data/ChIPPeak.csv')
-write.csv(anno, annoPeakTable, row.names = FALSE)
\ No newline at end of file
+write.table(anno, annoPeakTable, row.names = FALSE)
\ No newline at end of file
diff -r 982a01524118 -r 6a9b9694acbf annotate_peak/annotatePeak.xml
--- a/annotate_peak/annotatePeak.xml Thu Mar 16 16:13:45 2017 -0400
+++ b/annotate_peak/annotatePeak.xml Mon Mar 20 06:51:22 2017 -0400
@@ -5,11 +5,32 @@
- Rscript $__tool_directory__/annotatePeak.R "$DMR" "$annoPeakTable"
+ Rscript $__tool_directory__/annotatePeak.R "$DMR" "$annoData" "$bindingType" "$upstream" "$downstream" "$ignore.peak.strand" "$annoPeakTable"
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