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Update WMDA Nomenclature Data

Source: R/updateWmdaData.R
updateWmdaData.Rd

Downloads fresh WMDA nomenclature data from the IMGT/HLA GitHub repository and caches it locally for use by toSerology.

Usage

updateWmdaData(
  version = "Latest",
  cache_dir = NULL,
  force = FALSE,
  verbose = TRUE
)

Arguments

version

Character. The IMGT/HLA version to download. Default is "Latest" for the most recent release. Can also be a specific version tag (e.g., "3.54.0").

cache_dir

Character. Directory to store cached data. If NULL (default), uses the package's default cache location.

force

Logical. If TRUE, re-download even if cached data exists.

verbose

Logical. If TRUE (default), print progress messages.

Value

Invisibly returns the path to the cache directory.

Details

The WMDA nomenclature files are downloaded from: https://github.com/ANHIG/IMGTHLA

Downloaded files:

  • rel_dna_ser.txt: DNA to serology mappings

  • rel_ser_ser.txt: Broad to split relationships

  • hla_nom_p.txt: P-group definitions

The cache is stored as a single RDS file for fast loading. To clear the cache and revert to bundled data, delete the cache directory or set the environment variable DEEPMATCHR_CACHE_DIR to a new location.

See also

toSerology

Examples

# Show default cache directory (does not download)
cache_dir <- file.path(tempdir(), "wmda_test")
print(cache_dir)
#> [1] "/tmp/RtmpqyBOgk/wmda_test"

# \donttest{
# Update to latest WMDA data (requires internet)
updateWmdaData()
#> Downloading WMDA data (version: Latest)...
#>   Downloading rel_dna_ser.txt...
#>   Downloading rel_ser_ser.txt...
#>   Downloading hla_nom_p.txt...
#>   Saving to cache...
#> Done! Cached 27260 serology mappings, 23 split mappings, 18757 P-groups
#> Cache location: ~/.cache/deepMatchR

# Force re-download even if cache exists
updateWmdaData(force = TRUE)
#> Downloading WMDA data (version: Latest)...
#>   Downloading rel_dna_ser.txt...
#>   Downloading rel_ser_ser.txt...
#>   Downloading hla_nom_p.txt...
#>   Saving to cache...
#> Done! Cached 27260 serology mappings, 23 split mappings, 18757 P-groups
#> Cache location: ~/.cache/deepMatchR
# }