casper (version 2.6.0)

pathCounts: Compute exon path counts

Description

Compute counts for exon paths visited by aligned reads

Usage

pathCounts(reads, DB, mc.cores = 1, verbose=FALSE)

Arguments

reads

Object of class procBam containing aligned reads, as returned by procBam.

DB

Object of class annotatedGenome containing either a known or de novo annotated genome.

mc.cores

Number of processors to be used for parallel computing. Requires having package multicore installed and loaded.

verbose

Set to TRUE to print progress information.

Value

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.

Methods

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.

See Also

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.

Examples

##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--	or do  help(data=index)  for the standard data sets.