pathCounts {casper} | R Documentation

## 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.

### Author(s)

Camille Stephan-Otto Attolini

### 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.

[Package casper version 2.24.2 Index]