Function that maps biomarker identifiers from VCF variant annotation to full biomarker data tables for display in report — map_biomarker_data • PCGR

Function that maps biomarker identifiers from VCF variant annotation to full biomarker data tables for display in report

Usage

map_biomarker_data(
  varcalls = NULL,
  ref_data = NULL,
  settings = NULL,
  variant_origin = "Somatic",
  vartype = "snv_indel"
)

Arguments

varcalls: variant calls data frame with biomarker identifiers
ref_data: reference data object containing biomarker data
settings: PCGR settings object
variant_origin: variant origin for filtering biomarker evidence items (e.g. "Somatic", "Germline", "Any")
vartype: variant type for filtering biomarker evidence items (e.g. "snv_indel", "cna", "fusion")

Value

data frame with biomarker data for report display