binOverRegions: coverage of chromosome regions

In ChIPpeakAnno: Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments or any experiments resulted in large number of chromosome ranges

Description

calculate the coverage of 5'UTR, CDS and 3'UTR per transcript per bin.

Usage

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
)

Arguments

cvglists	A list of SimpleRleList or RleList. It represents the coverage for samples.
TxDb	An object of TxDb. It is used for extracting the annotations.
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.

Author(s)

Jianhong Ou

See Also

binOverGene, plotBinOverRegions

Examples

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)
}
}

ChIPpeakAnno documentation built on April 1, 2021, 6:01 p.m.