casper (version 2.6.0)

splitGenomeByLength: 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.

Value

List where each component is of class annotatedGenome.

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.

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)