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

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