mutation_types_identify: Identify Mutation Dictionary Used

In mutationtypes: Validate and Convert Mutational Impacts Using Standard Genomic Dictionaries

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'))

mutationtypes documentation built on May 29, 2024, 2:22 a.m.