Mercurial > repos > testtool > annotate_peak

diff annotate_peak/annotatePeak.R @ 16:ee3fc24b2108 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author testtool
date Thu, 16 Mar 2017 11:23:38 -0400
parents 53df7871db21
children 982a01524118
line wrap: on
line diff
--- a/annotate_peak/annotatePeak.R	Thu Mar 16 11:03:24 2017 -0400
+++ b/annotate_peak/annotatePeak.R	Thu Mar 16 11:23:38 2017 -0400
@@ -1,3 +1,8 @@
+require("ChIPseeker", quietly = TRUE)
+require("ChIPpeakAnno", quietly = TRUE)
+require("EnsDb.Hsapiens.v75", quietly = TRUE)
+require("GenomicRanges", quietly = TRUE)
+
 options(warn = -1)
 args <- commandArgs(trailingOnly = TRUE)
 DMR = args[1]
@@ -16,10 +21,6 @@
                     ranges = IRanges
                     (start = DMRInfo[, 2], end = DMRInfo[, 3]))
 peaks[1:2]
-## try http:// if https:// URLs are not supported
-source("https://bioconductor.org/biocLite.R")
-biocLite("EnsDb.Hsapiens.v75")
-library(EnsDb.Hsapiens.v75)
 annoData <- toGRanges(EnsDb.Hsapiens.v75)
 annoData[1:2]