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Tabulate SNVs by trinucleotide context

Source: R/trinuc_mutation_rates.R
trinuc_snv_counts.Rd

This function produces trinucleotide-context-specific SNV counts from MAF data for input to mutational signature extraction tools. Output can be tailored to meet formatting requirements of MutationalPatterns or deconstructSigs, which are probably similar to formats used by other tools.

Usage

trinuc_snv_counts(
  maf,
  genome,
  exclude_recurrent = FALSE,
  style = "MutationalPatterns"
)

Arguments

maf

a cancereffectsizeR-style MAF data table

genome

BSgenome reference genome (for looking up trinucleotide contexts)

exclude_recurrent

Default FALSE. When TRUE, only mutations private to each sample are included in counts, in order to reduce the influence of selection. (If you load more MAF data into the CESAnalysis later, recurrency may change.)

style

"MutationalPatterns" or "deconstructSigs"

Value

Matrix or data frame of SNV counts, suitable for use with MutationalPatterns or deconstructSigs. Samples with zero passing SNVs will not appear.