tally_mutations_96: Tally mutations in the 96 base substitution classes defined...

In nicolaroberts/nrmisc: Nicola Roberts miscellaneous functions

Description

Tally mutations in the 96 base substitution classes defined by trinucleotide context

Usage

tally_mutations_96(gr, genome, ref = "ref", alt = "alt",
  samp = "sampleID")

Arguments

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').

Value

A matrix of mutation counts with one row per sample and one column per base substitution class (trinucleotide context)

nicolaroberts/nrmisc documentation built on May 23, 2019, 5:09 p.m.