Mercurial > repos > testtool > annotate_peak
changeset 3:7beb1a8f7cb0 draft
Uploaded
| author | testtool |
|---|---|
| date | Mon, 27 Feb 2017 08:34:24 -0500 |
| parents | be66730c5c3b |
| children | e1c643f600d2 |
| files | annotatePeak/.Rhistory annotatePeak/._tool_dependencies.xml annotatePeak/tool_dependencies.xml |
| diffstat | 3 files changed, 60 insertions(+), 0 deletions(-) [+] |
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--- 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"))
--- 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>