# 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 @@
 <stdio>
    <exit_code range="1:" />
 </stdio>
-  <command> Rscript $__tool_directory__/annotatePeak.R "$DMR" "$annoPeakTable"</command>
+<command> Rscript $__tool_directory__/annotatePeak.R "$DMR" "$annoData"  "$bindingType"  "$upstream" "$downstream" "$ignore.peak.strand" "$annoPeakTable"</command>
   <inputs>
     <param optional="false" format="bed" name="DMR" type="data" value="" help="Bumphunter peaks." label="[required] file">
       <validator type="empty_field" message="This field is required."/>
     </param>
+    <param name="annoData" type="select" display="radio" label="annoData" help="choose your annoData human or mice">
+      <option name="human" type="text" value="EnsDb.Hsapiens.v75">Human</option>
+      <option name="mice" type="float" value="">Mice</option>
+    </param>
+    <param name="bindingType" type="select" display="radio" label="bindingType" help="choose bindingType">
+      <option name="sS" type="text" value="startSite">startSite</option>
+      <option name="eS" type="text" value="endSite">endSite</option>
+      <option name="fR" type="text" value="fullRange">fullRange</option>
+    </param>
+    <param name="ignore.peak.strand" type="select" display="radio" label="ignore.peak.strand" help="choose TRUE or FALSE">
+      <option name="T" type="text" value="TRUE">true</option>
+      <option name="F" type="text" value="FALSE">false</option>
+    </param>
+    <param name="upstream" type="float" value=""
+	       label="upstream - number no bigger than 0"
+	       help="e.g. '-5000'" >
+      </param>
+      <param name="downstream" type="float" value=""
+      	       label="downstream - number no less than 1"
+      	       help="e.g. '5000'" >
+            </param>
   </inputs>
   <outputs>
     <data format="csv" name="annoPeakTable" label="peakAnno.csv"/>