binOverRegions {ChIPpeakAnno} | R Documentation

## coverage of chromosome regions

### 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)
    }
    }

[Package ChIPpeakAnno version 3.26.4 Index]