splitGenomeByLength {casper} | R Documentation

## Split an annotatedGenome object into subsets according to gene length

### Description

`splitGenomeByLength` splits an annotatedGenome according to gene length (bp), which allows estimating the fragment start and length distribution for each subset separately.

### Usage

    splitGenomeByLength(DB, breaks=c(0,3000,5000,Inf))

### Arguments

`DB` | Object containing annotated genome. Must be of class `annotatedGenome`, as returned by `procGenome` or `createDenovoGenome`.
`breaks` | Breakpoints to define gene subgroups.

### Details

By default groups are <3000bp, 3000-5000bp, >5000bp, which work well for the human genome. Further sub-dividisions may result in unstable estimates of fragment start and length distributions.

### Value

List where each component is of class `annotatedGenome`.

### Author(s)

David Rossell

### See Also

`procGenome` and `createDenovoGenome` for creating `annotatedGenome` objects. `getDistrs` for estimating fragment start and length distribution.

### Examples

    ##Not run
    ## genDB<-makeTranscriptDbFromUCSC(genome="hg19", tablename="refGene")
    ## hg19DB <- procGenome(genDB, "hg19")
    ## hg19split <- splitGenomeByLength(hg19DB)

[Package casper version 2.18.0 Index]