A Comprehensive Toolkit for Clinical HLA Informatics
ambiguity_table_to_GLstring
GLstring_expand_longer
GLstring_gene_copies_combine
GLstring_genes_expanded
GLstring_genes
GLstring_genotype_ambiguity
GLstring_regex
GLstring_to_ambiguity_table
HLA_column_repair
HLA_columns_to_GLstring
HLA_match_number
HLA_match_summary_HCT
HLA_mismatch_alleles
HLA_mismatch_base
HLA_mismatch_logical
HLA_mismatch_number
HLA_mismatched_alleles
HLA_prefix_add
HLA_prefix_remove
HLA_truncate
HLA_validate
read_HML
A comprehensive toolkit for clinical Human Leukocyte Antigen (HLA) informatics, built on 'tidyverse' <https://tidyverse.tidyverse.org/> principles and making use of genotype list string (GL string, Mack et al. (2023) <doi:10.1111/tan.15126>) for storing and computing HLA genotype data. Specific functionalities include: coercion of HLA data in tabular format to and from GL string; calculation of matching and mismatching in all directions, with multiple output formats; automatic formatting of HLA data for searching within a GL string; truncation of molecular HLA data to a specific number of fields; and reading HLA genotypes in HML files and extracting the GL string. This library is intended for research use. Any application making use of this package in a clinical setting will need to be independently validated according to local regulations.
Useful links