splitGenomeByLength: Split an annotatedGenome object into subsets according to...
In casper: Characterization of Alternative Splicing based on Paired-End Reads

Description Usage Arguments Details Value Author(s) See Also Examples

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

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

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

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.

List where each component is of class annotatedGenome.

David Rossell

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

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

casper documentation built on Dec. 17, 2020, 2:01 a.m.