Prefix to add or remove from contig names in MAF file.
add
If prefix is used, default is to add prefix to contig names in MAF file. If false prefix will be removed from contig names.
ignoreChr
Chromsomes to remove from analysis. e.g. chrM
useSyn
Logical. Whether to include synonymous variants in analysis. Defaults to FALSE.
Value
A matrix of dimension nx96, where n is the number of samples in the MAF.
Details
Extracts immediate 5' and 3' bases flanking the mutated site and classifies them into 96 substitution classes.
This function loads reference genome into memeory. Typical human geneome occupies a peak memory of ~3 gb while extracting bases.