pathCounts {casper} | R Documentation |
Compute counts for exon paths visited by aligned reads
pathCounts(reads, DB, mc.cores = 1, verbose=FALSE)
reads |
Object of class |
DB |
Object of class |
mc.cores |
Number of processors to be used for parallel computing. Requires
having package |
verbose |
Set to |
Named integer vector with counts of exon paths. Names are character strings built as ".exon1.exon2-exon3.exon4.", with dashes making the split between exons visited by left and right-end reads correspondingly.
signature(reads='list')
Computes counts for exon paths from a list of procBam objects (usually reads processed and split by chromosome).
signature(reads='procBam')
Compute counts for exon paths from a procBam object of processed reads.
Camille Stephan-Otto Attolini
procGenome
to create an annotated genome object,
createDenovoGenome
to create a de novo annotated genome.
See help(getNreads) to get number of fragments mapping to each island.
##---- Should be DIRECTLY executable !! ---- ##-- ==> Define data, use random, ##-- or do help(data=index) for the standard data sets.