mutation_types_convert_so_to_maf {mutationtypes}

Convert SO Mutation Types to MAF

Description

Convert SO Mutation Types to MAF

Usage

mutation_types_convert_so_to_maf(
  so_mutation_types,
  variant_type = NULL,
  inframe = NULL,
  split_on_ampersand = TRUE,
  missing_to_silent = FALSE,
  verbose = TRUE
)

Arguments

so_mutation_types

a vector of SO 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)

inframe

is the mutation inframe? (logical). Used to map protein_altering_variant to valid MAF columns

split_on_ampersand

should '&' separated SO terms be automatically converted to single SO 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_so_to_maf(c('INTRAGENIC', 'INTRAGENIC', 'intergenic_region'))