splitGenomeByLength {casper} | R Documentation |
splitGenomeByLength
splits an annotatedGenome according to gene
length (bp), which allows estimating the fragment start and length
distribution for each subset separately.
splitGenomeByLength(DB, breaks=c(0,3000,5000,Inf))
DB |
Object containing annotated genome. Must be of class
|
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)