Package: immunogenetr 0.1.0

Nicholas Brown

immunogenetr: A Comprehensive Toolkit for Clinical HLA Informatics

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.

Authors:Nicholas Brown [cre, aut], Busra Coskun [aut]

immunogenetr_0.1.0.tar.gz
immunogenetr_0.1.0.tar.gz(r-4.5-noble)immunogenetr_0.1.0.tar.gz(r-4.4-noble)
immunogenetr_0.1.0.tgz(r-4.4-emscripten)immunogenetr_0.1.0.tgz(r-4.3-emscripten)
immunogenetr.pdf |immunogenetr.html✨
immunogenetr/json (API)
NEWS

# Install 'immunogenetr' in R:
install.packages('immunogenetr', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/k96nb01/immunogenetr_package/issues

Datasets:
  • HLA_dictionary - Data on HLA alleles in the 2008 HLA dictionary
  • HLA_typing_1 - Synthetic HLA typing data for 10 individuals for the HLA-A, B, C, DRB1, DRB3/4/5, DQB1, DQA1, DPB1 and DPA1 loci.
  • HLA_typing_LIS - Synthetic HLA typing data for 10 individuals for the HLA-A, B, C, DRB1, DRB3, DRB4, DRB5, DQB1, DQA1, DPB1 and DPA1 loci. Data formatted to resemble a HistoTrac table.
  • Haplotype_frequencies - Ten HLA-A~C~B~DRB3/4/5~DRB1~DQA1~DQB1~DPA1~DPB1 haplotypes and their frequencies in the global population.
  • mismatch_table_2010 - Consensus mismatch numbers for every possible allele combination at a single locus, from the 2010 publication.
  • mismatch_table_2016 - Consensus mismatch numbers for every possible allele combination at a single locus, from the 2016 publication.

On CRAN:

Conda:

1.70 score 20 exports 22 dependencies

Last updated 5 hours agofrom:854e20e4e9. Checks:3 OK. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 24 2025
R-4.5-linuxOKMar 24 2025
R-4.4-linuxOKMar 24 2025

Exports:ambiguity_table_to_GLstringGLstring_expand_longerGLstring_gene_copies_combineGLstring_genesGLstring_genes_expandedGLstring_genotype_ambiguityGLstring_regexHLA_column_repairHLA_columns_to_GLstringHLA_match_numberHLA_match_summary_HCTHLA_mismatch_baseHLA_mismatch_logicalHLA_mismatch_numberHLA_mismatched_allelesHLA_prefix_addHLA_prefix_removeHLA_truncateHLA_validateread_HML

Dependencies:clicpp11dplyrfansigenericsgluelifecyclemagrittrpillarpkgconfigpurrrR6rlangstringistringrtibbletidyrtidyselectutf8vctrswithrxml2

Readme and manuals

Help Manual

Help pageTopics
ambiguity_table_to_GLstringambiguity_table_to_GLstring
GLstring_expand_longerGLstring_expand_longer
GLstring_gene_copies_combineGLstring_gene_copies_combine
GLstring_genesGLstring_genes
GLstring_genes_expandedGLstring_genes_expanded
GLstring_genotype_ambiguityGLstring_genotype_ambiguity
GLstring_regexGLstring_regex
Ten HLA-A~C~B~DRB3/4/5~DRB1~DQA1~DQB1~DPA1~DPB1 haplotypes and their frequencies in the global population.Haplotype_frequencies
HLA_column_repairHLA_column_repair
HLA_columns_to_GLstringHLA_columns_to_GLstring
Data on HLA alleles in the 2008 HLA dictionaryHLA_dictionary
HLA_match_numberHLA_match_number
HLA_match_summary_HCTHLA_match_summary_HCT
HLA_mismatch_baseHLA_mismatch_base
HLA_mismatch_logicalHLA_mismatch_logical
HLA_mismatch_numberHLA_mismatch_number
HLA_mismatched_allelesHLA_mismatched_alleles
HLA_prefix_addHLA_prefix_add
HLA_prefix_removeHLA_prefix_remove
HLA_truncateHLA_truncate
Synthetic HLA typing data for 10 individuals for the HLA-A, B, C, DRB1, DRB3/4/5, DQB1, DQA1, DPB1 and DPA1 loci.HLA_typing_1
Synthetic HLA typing data for 10 individuals for the HLA-A, B, C, DRB1, DRB3, DRB4, DRB5, DQB1, DQA1, DPB1 and DPA1 loci. Data formatted to resemble a HistoTrac table.HLA_typing_LIS
HLA_validateHLA_validate
Consensus mismatch numbers for every possible allele combination at a single locus, from the 2010 publication.mismatch_table_2010
Consensus mismatch numbers for every possible allele combination at a single locus, from the 2016 publication.mismatch_table_2016
read_HMLread_HML