coverageMatrixListFromGAL {AllelicImbalance} | R Documentation |
Get coverage per nucleotide for reads covering a region
coverageMatrixListFromGAL(BamList, ...) ## S4 method for signature 'GAlignmentsList' coverageMatrixListFromGAL(BamList, strand = "*", ignore.empty.bam.row = TRUE)
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 |
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.
Jesper R. Gadin
r <- reads seqlevels(r) <- '17' covMatList <- coverageMatrixListFromGAL(BamList=r, strand='+')