Description Usage Arguments Value
Tally mutations in the 96 base substitution classes defined by trinucleotide context
1 2 | tally_mutations_96(gr, genome, ref = "ref", alt = "alt",
samp = "sampleID")
|
gr |
A GRanges object with ranges of width 1 (variant positions) and at least three metadata columns for reference base, alternate base, and sample name. |
genome |
A BSgenome object of the reference genome to use for trinucleotide context calculations (e.g. 'BSgenome.Hsapiens.UCSC.hg19::BSgenome.Hsapiens.UCSC.hg19') |
ref |
Variable name for the reference base column in gr (default 'ref'). |
alt |
Variable name for the alternative base column in gr (default 'alt'). |
samp |
Variable name for the sample ID column in gr (default 'sampleID'). |
A matrix of mutation counts with one row per sample and one column per base substitution class (trinucleotide context)
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