mutation_types_identify {mutationtypes}

Identify Mutation Dictionary Used

Description

Looks at variant consequence terms and guesses what mutation dictionary was used. SO and PAVE dictionaries overlap, meaning an observed set of terms can perfectly match both ontologies. If this happens, we assume they are SO terms.

Usage

mutation_types_identify(
  mutation_types,
  split_on_ampersand = TRUE,
  verbose = TRUE,
  ignore_missing = FALSE
)

Arguments

mutation_types

mutation types to test (character)

split_on_ampersand

split mutation types in a single string separated by ampersand (&) into 2 distinct mutation type columns (flag)

verbose

verbose (flag)

ignore_missing

should we ignore missing (NA) or empty (”) mutation_types when identifying a classification scheme (flag)

Value

one of c('SO', 'MAF', 'UNKNOWN'). Will return 'UNKNOWN' unless ALL mutation types fit with one of the supported dictionaries

Examples

mutation_types_identify(c('bob', 'billy', 'missense_variant'))