Process OncoKB fusion output file and fetch complete annotations — process_oncokb_fusion • PCGR

Process OncoKB fusion output file and fetch complete annotations

Usage

process_oncokb_fusion(
  fusion_file = NULL,
  var_calls = NULL,
  oncotree_code = NULL,
  oncokb_token = NULL,
  rate_limiting_delay = 1
)

Arguments

fusion_file: Path to OncoKB-annotated fusion file (TSV format)
var_calls: Data frame with variant calls (used for mapping of variant alteration)
oncotree_code: OncoTree code/name (e.g., "SKIN", "BREAST")
oncokb_token: OncoKB API token
rate_limiting_delay: Delay in seconds between API calls to respect rate limits (default: 1 second)

Value

List with fusion information and corresponding JSON annotations