diff annotate_peak/annotatePeak.R @ 12:54e19bceff70 draft

Uploaded
author testtool
date Thu, 16 Mar 2017 07:21:37 -0400
parents
children 77c0aee75ac6
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/annotate_peak/annotatePeak.R	Thu Mar 16 07:21:37 2017 -0400
@@ -0,0 +1,26 @@
+require("ChIPseeker", quietly = TRUE)
+require("ChIPpeakAnno", quietly = TRUE)
+require("org.Hs.eg.db", quietly = TRUE)
+require("GenomicRanges", 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 = ""
+)
+
+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"))
+
+write.csv(annotatePeak, annoPeakTable, row.names = FALSE)