Overview | Setup | Converting tabular HLA data to GL strings | Splitting GL strings into loci | Calculating HLA mismatches | Is there a mismatch? (HLA_mismatch_logical) | How many mismatches? (HLA_mismatch_number) | Which alleles are mismatched? (HLA_mismatched_alleles) | Match count (HLA_match_number) | HLA match summaries for transplantation | Finding the best donor | Working with HLA allele names | Truncation | Prefix management | Regex for GL string searching | Column name repair | Reading HML files | Disclaimer
Package: immunogenetr 1.3.0
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. 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.
Authors:
immunogenetr_1.3.0.tar.gz
immunogenetr_1.3.0.zip(r-4.7)immunogenetr_1.3.0.zip(r-4.6)immunogenetr_1.3.0.zip(r-4.5)
immunogenetr_1.3.0.tgz(r-4.6-any)immunogenetr_1.3.0.tgz(r-4.5-any)
immunogenetr_1.3.0.tar.gz(r-4.7-any)immunogenetr_1.3.0.tar.gz(r-4.6-any)
immunogenetr_1.3.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
immunogenetr/json (API)
| # Install 'immunogenetr' in R: |
| install.packages('immunogenetr', repos = c('https://k96nb01.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/k96nb01/immunogenetr_package/issues
Pkgdown/docs site:https://immunogenetr.org
Datasets:
- Haplotype_frequencies - Ten HLA-A~C~B~DRB3/4/5~DRB1~DQA1~DQB1~DPA1~DPB1 haplotypes and their frequencies in the global population.
- 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.
- 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.
hlahla-typinginformaticstidyverse
Last updated from:4b2364fa5f. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 137 | ||
| source / vignettes | OK | 159 | ||
| linux-release-x86_64 | OK | 143 | ||
| macos-release-arm64 | OK | 128 | ||
| macos-oldrel-arm64 | OK | 190 | ||
| windows-devel | OK | 90 | ||
| windows-release | OK | 100 | ||
| windows-oldrel | OK | 93 | ||
| wasm-release | OK | 123 |
Exports:ambiguity_table_to_GLstringGLstring_expand_longerGLstring_gene_copies_combineGLstring_genesGLstring_genes_expandedGLstring_genotype_ambiguityGLstring_regexGLstring_to_ambiguity_tableHLA_column_repairHLA_columns_to_GLstringHLA_match_numberHLA_match_summary_HCTHLA_mismatch_allelesHLA_mismatch_baseHLA_mismatch_logicalHLA_mismatch_numberHLA_mismatched_allelesHLA_prefix_addHLA_prefix_removeHLA_truncateHLA_validateread_HML
Dependencies:clicpp11dplyrgenericsgluelifecyclemagrittrpillarpkgconfigpurrrR6rlangstringistringrtibbletidyrtidyselectutf8vctrswithrxml2
