Changelog
Source:NEWS.md
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()
)
- Encode/lookup Multiple Allele Codes (
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 0.2.2
- 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 inupscale_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()
andlookup_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 NMDPNew
gl_to_df()
anddf_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-formedNew
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. Theextract_alleles()_*
functions also usecount_alleles()
to warn whenever they encounter a typing with more than two alleles per locus.
- Use
hlapro 0.1.0
- New
get_mismatches()
determines mismatched antigens from a pair of donor/recipient typings.