AllelicImbalance (version 1.10.2)

coverageMatrixListFromGAL: coverage matrix of GAlignmentsList

Description

Get coverage per nucleotide for reads covering a region

Usage

coverageMatrixListFromGAL(BamList, ...)
"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.

Examples

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