Mercurial > repos > kpbioteam > chipeakanno_annopeaks

diff chipeakanno_annopeaks.R @ 7:17b814d78ac6 draft

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planemo upload for repository https://github.com/kpbioteam/chipeakanno_annopeaks commit 5ee10ba73cd634a41b84f059f02edeaa04f69b8d-dirty
author kpbioteam
date Thu, 21 Jun 2018 10:08:06 -0400
parents b5bc7e70b949
children 0473a72c943c
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--- a/chipeakanno_annopeaks.R	Wed Jun 20 06:59:04 2018 -0400
+++ b/chipeakanno_annopeaks.R	Thu Jun 21 10:08:06 2018 -0400
@@ -1,8 +1,3 @@
-source("https://bioconductor.org/biocLite.R")
-biocLite("ChIPpeakAnno")
- 
-biocLite("rtracklayer")
-
 require("ChIPpeakAnno", quietly = TRUE)
 require("EnsDb.Hsapiens.v75", quietly = TRUE)
 require("rtracklayer", quietly = TRUE)
@@ -21,7 +16,7 @@
 DMRInfo <-  read.table(input1)
 peaks <- GRanges(seqnames = DMRInfo[, 1],
                     ranges = IRanges
-                    (start = DMRInfo[, 2], end = DMRInfo[, 3]))
+                    (start = DMRInfo[, 2], end = DMRInfo[, 3],score=DMRInfo[, 9]))
 
 annoData <- toGRanges(EnsDb.Hsapiens.v75)
 seqlevelsStyle(peaks) <- seqlevelsStyle(annoData)