Extract mutation effect information — extract_complete

param oncokb_annotation OncoKB annotation list param variant_id Variant identifier return Tibble with mutation effect data export Extract oncogenicity classification

Usage

extract_complete_annotation(
  oncokb_annotation,
  gene = NA,
  alteration = NA,
  vartype = NA,
  oncotree_code = NA,
  variant_id = NA,
  match_by = "hgvsp"
)

Arguments

oncokb_annotation: OncoKB annotation list
gene: gene symbol / gene fusion
alteration: alteration description (e.g., HGVSp short format for SNVs/InDels)
vartype: variant type (e.g., "snv_indel", "fusion", "cna")
oncotree_code: OncoTree code for tumor type
variant_id: Variant identifier
match_by: Matching strategy for SNVs/InDels (e.g., "hgvsp", "genomic")

Value

Named list with all extracted components

Details

param oncokb_annotation OncoKB annotation list param variant_id Variant identifier return Tibble with oncogenicity data export Extract clinical summaries

param oncokb_annotation OncoKB annotation list param variant_id Variant identifier return Tibble with summary text fields export Extract complete structured annotation from OncoKB JSON