Process OncoKB CNA output file and fetch complete annotations — process_oncokb_cna • PCGR

Process OncoKB CNA output file and fetch complete annotations

Usage

process_oncokb_cna(
  cna_file,
  oncotree_code = NULL,
  oncokb_token = NULL,
  var_calls = NULL,
  rate_limiting_delay = 1
)

Arguments

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

Value

List with CNA information and corresponding JSON annotations