coverageMatrixListFromGAL: coverage matrix of GAlignmentsList

In AllelicImbalance: Investigates Allele Specific Expression

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='+')

AllelicImbalance documentation built on Nov. 8, 2020, 6:52 p.m.