binOverGene: coverage of gene body

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 gene body per gene per bin.

Usage

binOverGene(
  cvglists,
  TxDb,
  upstream.cutoff = 0L,
  downstream.cutoff = upstream.cutoff,
  nbinsGene = 100L,
  nbinsUpstream = 20L,
  nbinsDownstream = nbinsUpstream,
  includeIntron = FALSE,
  minGeneLen = nbinsGene,
  maxGeneLen = 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.
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.

Author(s)

Jianhong Ou

See Also

binOverRegions, 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 <- binOverGene(cvglists, TxDb.Hsapiens.UCSC.hg19.knownGene)
plotBinOverRegions(d)
}
}

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