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Function that loads specific set of clinical variant evidence items (CIViC + CGI) based on given parameters (mutation type, variant origin, tumor type etc)

Usage

load_eitems(
  eitems_raw = NULL,
  ontology = NULL,
  alteration_type = "MUT",
  origin = "Somatic",
  tumor_type_specificity = NULL,
  tumor_type = NULL
)

Arguments

eitems_raw

complete set of clinical variant evidence items

ontology

phenotype ontology data frame

alteration_type

type of alteration ('MUT', 'CNA', 'MUT_LOF')

origin

variant origin ('Somatic','Germline')

tumor_type_specificity

tumor type specificity ('any', 'specific')

tumor_type

primary tumor site

Value

eitems variant evidence items