# HG changeset patch
# User testtool
# Date 1488202464 18000
# Node ID 7beb1a8f7cb047896aabcaf04f5b078ce3cdad57
# Parent  be66730c5c3bc22b4a076bb58eda146ac83733db
Uploaded

diff -r be66730c5c3b -r 7beb1a8f7cb0 annotatePeak/.Rhistory
--- 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"))
diff -r be66730c5c3b -r 7beb1a8f7cb0 annotatePeak/._tool_dependencies.xml
Binary file annotatePeak/._tool_dependencies.xml has changed
diff -r be66730c5c3b -r 7beb1a8f7cb0 annotatePeak/tool_dependencies.xml
--- a/annotatePeak/tool_dependencies.xml	Sat Feb 25 11:29:01 2017 -0500
+++ b/annotatePeak/tool_dependencies.xml	Mon Feb 27 08:34:24 2017 -0500
@@ -188,6 +188,9 @@
                       <package sha256sum="fcedc27233ec2875e046941f0e2453fcfe22f07a3b5a086bebcfab8b1e748c2e">
                           https://bioarchive.galaxyproject.org/ChIPpeakAnno_3.9.3.tar.gz
                       </package>
+                      <package sha256sum="d40f23c90db4a72b721de6a42cc29a0cfab0474d34af36c5083c29eaf21f65df">
+                          https://bioarchive.galaxyproject.org/software/bioconductor-chipseeker/
+                      </package>
                       <package sha256sum="f524148fdb29aac3a178618f88718d3d4ac91283014091aa11a01f1c70cd4e51">
                           https://depot.galaxyproject.org/software/locfit/locfit_1.5-9.1.tar.gz
                       </package>