mutation_types_convert_pave_to_maf {mutationtypes}

Convert PAVE Mutation Types to MAF

Description

Convert PAVE Mutation Types to MAF

Usage

mutation_types_convert_pave_to_maf(
  pave_mutation_types,
  variant_type = NULL,
  split_on_ampersand = TRUE,
  missing_to_silent = FALSE,
  verbose = TRUE
)

Arguments

pave_mutation_types

a vector of PAVE terms you want to convert to MAF variant classifications (character)

variant_type

a vector describing each mutations type. Valid elements include: "SNP", "DNP", "TNP", "ONP", "DEL", "INS". Used to map frameshift_variant to more specific MAF columns (character)

split_on_ampersand

should '&' separated PAVE terms be automatically converted to single PAVE terms based on highest severity? (flag)

missing_to_silent

should missing (NA) or empty (”) mutation types be converted to 'Silent' mutations?

verbose

verbose (flag)

Value

matched MAF variant classification terms (character)

Examples

mutation_types_convert_pave_to_maf(
  c('upstream_gene_variant', 'stop_lost', 'splice_acceptor_variant')
)