Process OncoKB MAF output files (both HGVSp and HGVSg) and fetch complete annotations

Process OncoKB MAF output files (both HGVSp and HGVSg) and fetch complete annotations

Usage

process_oncokb_maf(
  maf_file_hgvsp = NULL,
  maf_file_hgvsg = NULL,
  var_calls = NULL,
  oncotree_code = NULL,
  oncokb_token = NULL,
  oncokb_base_api_url = NULL,
  rate_limiting_delay = 1
)

Arguments

maf_file_hgvsp

Path to OncoKB-annotated MAF file using HGVSp (protein change) (optional)

maf_file_hgvsg

Path to OncoKB-annotated MAF file using HGVSg (genomic change) (optional)

var_calls

Data frame with variant calls (used for mapping of variant alteration)

oncotree_code

OncoTree code used for OncoKB annotation

oncokb_token

OncoKB API token

oncokb_base_api_url

Optional base URL for OncoKB API (default: oncokb_base_api_url)

rate_limiting_delay

Delay in seconds between API calls to respect rate limits (default: 1 second)

Value

Data frame with variant information and corresponding JSON annotations