binOverGene {ChIPpeakAnno} | R Documentation |
calculate the coverage of gene body per gene per bin.
binOverGene(cvglists, TxDb, upstream.cutoff = 0L, downstream.cutoff = upstream.cutoff, nbinsGene = 100L, nbinsUpstream = 20L, nbinsDownstream = nbinsUpstream, includeIntron = FALSE, minGeneLen = nbinsGene, maxGeneLen = 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. |
nbinsGene, nbinsUpstream, nbinsDownstream |
The number of bins for gene, upstream and downstream. |
includeIntron |
A logical value which indicates including intron or not. |
minGeneLen, maxGeneLen |
minimal or maximal length of gene. |
Jianhong Ou
binOverRegions, 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 <- binOverGene(cvglists, TxDb.Hsapiens.UCSC.hg19.knownGene) plotBinOverRegions(d) } }