coverageMatrixListFromGAL {AllelicImbalance} | R Documentation

## coverage matrix of GAlignmentsList

### Description

Get coverage per nucleotide for reads covering a region

### Usage

    coverageMatrixListFromGAL(BamList, ...)

    ## S4 method for signature 'GAlignmentsList'
    coverageMatrixListFromGAL(BamList, strand = "*", ignore.empty.bam.row = TRUE)

### Arguments

`BamList` | GAlignmentsList containing reads over the region to calculate coverage
`...` | arguments to pass on
`strand` | strand has to be '+' or '-'
`ignore.empty.bam.row` | argument not in use atm

### Details

a convenience function to get the coverage from a list of reads stored in GAlignmnetsList, and returns by default a list with one matrix, and information about the genomic start and stop positions.

### Author(s)

Jesper R. Gadin

### Examples

    r <- reads
    seqlevels(r) <- '17'
    covMatList <- coverageMatrixListFromGAL(BamList=r, strand='+')

[Package AllelicImbalance version 1.25.2 Index]