binOverRegions {ChIPpeakAnno} | R Documentation |
calculate the coverage of 5'UTR, CDS and 3'UTR per transcript per bin.
binOverRegions( cvglists, TxDb, upstream.cutoff = 1000L, downstream.cutoff = upstream.cutoff, nbinsCDS = 100L, nbinsUTR = 20L, nbinsUpstream = 20L, nbinsDownstream = nbinsUpstream, includeIntron = FALSE, minCDSLen = nbinsCDS, minUTRLen = nbinsUTR, maxCDSLen = Inf, maxUTRLen = Inf )
cvglists |
A list of SimpleRleList or RleList. It represents the coverage for samples. |
TxDb |
An object of |
upstream.cutoff, downstream.cutoff |
cutoff length for upstream or downstream of transcript. |
nbinsCDS, nbinsUTR, nbinsUpstream, nbinsDownstream |
The number of bins for CDS, UTR, upstream and downstream. |
includeIntron |
A logical value which indicates including intron or not. |
minCDSLen, minUTRLen |
minimal length of CDS or UTR of transcript. |
maxCDSLen, maxUTRLen |
maximal length of CDS or UTR of transctipt. |
Jianhong Ou
binOverGene, plotBinOverRegions
if(Sys.getenv("USER")=="jianhongou"){ path <- system.file("extdata", package="ChIPpeakAnno") library(TxDb.Hsapiens.UCSC.hg19.knownGene) library(rtracklayer) files <- dir(path, "bigWig") if(.Platform$OS.type != "windows"){ cvglists <- lapply(file.path(path, files), import, format="BigWig", as="RleList") names(cvglists) <- sub(".bigWig", "", files) d <- binOverRegions(cvglists, TxDb.Hsapiens.UCSC.hg19.knownGene) plotBinOverRegions(d) } }