Changelog

Source: NEWS.md

hlapro 0.4.2

• Fix v3 allele groups with 4 digits incorrectly recognized as v2
• When comparing two sets of alleles, reorder_alleles() did some unnecessary reordering when NAs were present.
• Add extended mode to get_resolution for intermediate alleles; now distinguishes between CALs and MACs

hlapro 0.4.1

• Fix load_eplet_registry() for new release of HLA Eplet registry (2025-02-01)
  • Version information is now communicated differently
  • Small updates to column/content order
  • “All alleles” column is no longer included (7112cde5)
• Update clean_hla() to also convert deleted/changed alleles
• Minor fixes to clean_hla() conversion of v2 alleles

hlapro 0.4.0

• Update clean_hla() to also convert pre-2010 typings (v2) to the current nomenclature (v3)
• Fix load_eplet_registry() for new release of HLA Eplet registry (2024-08-30)
• Wrap the py-ard python package to:
  • Encode/lookup Multiple Allele Codes (mac_lookup(), mac_expand())
  • Reduce alleles to serological equivalents (reduce_to_serology())
  • Reduce alleles to 2-field (ARD) level (reduce_to_field2())

hlapro 0.3.0

• New read_lum_csv() function to parse raw Luminex Single-Antigen Bead assay data
• Fixed tests for new release of HLA Eplet registry (2024-08-19)

hlapro 0.2.3

• Fixed tests for new release of HLA Eplet registry (2024-03-15)

hlapro 0.2.2

• Updated for new release of the HLA Eplet registry: incorporating papers by Bezstarosti et al. and Osoegawa et al. (#11)

hlapro 0.2.1

• Fixed check for input_loci argument in upscale_typings() (#10).

hlapro 0.2.0

• New functions to lookup eplets/alleles in the HLA Eplet registry. Updated for release “2024-01-22: IPD-IMGT/HLA 3.54” of the registry (#9)

  • load_eplet_registry() scrapes the database from the website, or loads an existing version from disk
  • lookup_alleles() and lookup_eplets() return the eplets that occur on an input vector of HLA alleles, or vice versa.
  • get_positive_eplets() returns eplets that occur on positive (but not negative) beads for a dataframe of Luminex results.

• New upscale_typings() function to impute high-resolution (two-field) genotypes for a low resolution serological input typing, based on haplotype frequencies released by the NMDP

• New gl_to_df() and df_to_gl() functions to convert between a data frame with one column per allele and a GL String containing all alleles.

• New clean_hla() function to correct common formatting issues in HLA allele typing strings.

• New functions to get serological equivalents of an allele from the ETRL HLA tables. These tables are also shipped with the package as the etrl_hla data frame:

  • get_serology() for the split or else the broad-level serology
  • get_broad() for the broad-level serology
  • get_split() for the split-level serology
  • get_public() for the Bw4 or Bw6 epitope

• New validate_alleles() to check whether a(n) (list of) HLA allele(s) is well-formed

• New get_resolution() to determine resolution of a(n) (list of) HLA allele(s) as either low, intermediate, or high.

• New extract_alleles_str(), extract_alleles_df() gets alleles for each locus from HLA typing string, and separates them into named list elements / new columns in a data frame.

  • Use count_alleles() to inspect the number of alleles per locus. The extract_alleles()_* functions also use count_alleles() to warn whenever they encounter a typing with more than two alleles per locus.

hlapro 0.1.0

• New get_mismatches() determines mismatched antigens from a pair of donor/recipient typings.