mut_192_occurrences: Count 192 trinucleotide mutation occurrences

In MutationalPatterns: Comprehensive genome-wide analysis of mutational processes

Description

@details This function is called by mut_matrix_stranded. The 192 trinucleotide context is the 96 trinucleotide context combined with the strands. This function calculates the 192 trinucleotide context for all variants. and then splits these per GRanges (samples). It then calculates how often each 192 trinucleotide context occurs.

Usage

mut_192_occurrences(type_context, strand, gr_sizes)

Arguments

type_context	result from type_context function
strand	factor with strand information for each position, for example "U" for untranscribed, "T" for transcribed strand, and "-" for unknown
gr_sizes	A vector indicating the number of variants per GRanges

Value

Mutation matrix with 192 mutation occurrences and 96 trinucleotides for two strands

MutationalPatterns documentation built on Nov. 14, 2020, 2:03 a.m.