diff annotate_peak/annotatePeak.R @ 14:4a489b0d247f draft

Uploaded
author testtool
date Thu, 16 Mar 2017 10:59:08 -0400
parents 77c0aee75ac6
children 53df7871db21
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line diff
--- a/annotate_peak/annotatePeak.R	Thu Mar 16 07:28:01 2017 -0400
+++ b/annotate_peak/annotatePeak.R	Thu Mar 16 10:59:08 2017 -0400
@@ -1,9 +1,4 @@
-require("ChIPseeker", quietly = TRUE)
-require("ChIPpeakAnno", quietly = TRUE)
-
 options(warn = -1)
-options("download.file.method"="wget")
-
 args <- commandArgs(trailingOnly = TRUE)
 DMR = args[1]
 annoPeakTable = args[2]
@@ -17,12 +12,23 @@
   quote = ""
 )
 
-DMRPeaks <- GRanges(seqnames = DMRInfo[, 1],
+peaks <- GRanges(seqnames = DMRInfo[, 1],
                     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]
 
-annotatePeak <-
-  as.data.frame(annotatePeak(DMRPeaks, level = "gene", annoDb = "org.Hs.eg.db"))
+## keep the seqnames in the same style
+seqlevelsStyle(peaks) <- seqlevelsStyle(annoData)
+## do annotation by nearest TSS
+anno <- annotatePeakInBatch(peaks, AnnotationData=annoData)
+anno[1:2]
+annoPeakTable <- ('test-data/ChIPPeak.csv')
+write.csv(anno, annoPeakTable, row.names = FALSE)
 
-annoPeakTable <- ('test-data/annoPeakTable.csv')
-write.csv(annotatePeak, annoPeakTable, row.names = FALSE)
+