Package: HLAtools 1.11.0

HLAtools: Toolkit for HLA Immunogenomics

A toolkit for the analysis and management of data for genes in the so-called "Human Leukocyte Antigen" (HLA) region. Functions extract reference data from the Anthony Nolan HLA Informatics Group/ImmunoGeneTics HLA 'GitHub' repository (ANHIG/IMGTHLA) <https://github.com/ANHIG/IMGTHLA>, validate Genotype List (GL) Strings, convert between UNIFORMAT and GL String Code (GLSC) formats, translate HLA alleles and GLSCs across ImmunoPolymorphism Database (IPD) IMGT/HLA Database release versions, identify differences between pairs of alleles at a locus, generate customized, multi-position sequence alignments, trim and convert allele-names across nomenclature epochs, and extend existing data-analysis methods. Tran et al., (2025) <doi:10.1111/iji.70013>.

Authors:Livia Tran [aut], Ryan Nickens [aut], Leamon Crooms IV [aut], Derek Pappas [aut], Vinh Luu [ctb], Josh Bredeweg [ctb], Steven Mack [aut, cre]

HLAtools_1.11.0.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
HLAtools/json (API)

# Install 'HLAtools' in R:

install.packages('HLAtools', repos = c('https://sjmack.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/sjmack/hlatools/issues

Datasets:

alleleListHistory - Allele Names Across All Release Versions
fragmentFeatureNames - Gene Features of HLA Pseudogenes and Gene Fragments
GLSC.ex - Example Data Frame of Genotype List String Code Data
GLstring.ex - Example Data Frame of Genotype List String Data.
HLAatlas - Boundary Positions of Exons, Introns and UTRs in Amino Acid, cDNA and gDNA Alignments
HLAgazetteer - Functional and Organizational Categories of Genes Supported by the IPD-IMGT/HLA Database
IMGTGenomicReferences - Genomic Reference Alleles for each Gene in the IPD-IMGT/HLA Database
IMGTHLAGeneTypes - Molecular characteristics of the Genes Curated by the IPD-IMGT/HLA Database
sHLAdata - Synthetic HLA Data for use with Package Examples
UNIFORMAT.example - Example Data Frame of UNIFORMAT Data.

On CRAN:

5.86 score 4 stars 1 packages 20 scripts 373 downloads 73 exports 63 dependencies

Last updated from:0ce07c13e5. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	177
source / vignettes	OK	241
linux-release-x86_64	OK	205
macos-release-arm64	OK	155
macos-oldrel-arm64	OK	134
windows-devel	OK	156
windows-release	OK	136
windows-oldrel	OK	143
wasm-release	OK	135

Exports:addCodonLine alignmentFull alignmentSearch alleleTrim atlasFull atlasMaker BDstrat BDtoPyPop buildAlignments buildGazetteer buildGenomicReferences buildIMGTHLAGeneTypes checkAlignType checkgDNAstart checkSource checkVersion compareSequences convertAny countSpaces customAlign expandVersion ffN formatHead getAlignmentNames getField getLatestVersion GIANT GLStoUNI GLtoUN GLupdate GLV GLV2 GLvalidate GLVhelper motifMatch multiAlign multiAlleleTrim multiGLStoUNI multiLocusValidation multiQueryRelease multiSearch multiTranslateGLstring multiUNItoGLS multiUpdateGL numFields parseAlignmentHead posSort pypopHeaders queryPositions queryRelease redec relRisk repoVersion squashVersion translateAllele translateGLstring typeToSource uniAlign uniSearch UNItoGLS UNtoGL updateAll updateAlleleListHistory updateGL validateAllele validateGLstring validateLocus validateMotif validatePositions validateUniformat validateVersion variantTable verifyAllele

Dependencies:askpass bit bit64 boot cellranger class cli clipr cpp11 crayon curl data.table DescTools dplyr e1071 Exact expm fmsb forcats fs generics gld glue haven hms httr jsonlite lattice lifecycle lmom magrittr MASS Matrix mime mvtnorm openssl pillar pkgconfig prettyunits progress proxy R6 Rcpp readr readxl rematch rlang rootSolve rstudioapi rvest selectr stringi stringr sys tibble tidyselect tzdb utf8 vctrs vroom withr xfun xml2

HLAtools

Rendered fromHLAtools.Rmdusingknitr::rmarkdown

Last update: 2026-07-21
Started: 2024-03-25

Help page	Topics
Add an 'AA codon' Line to Alignments When Missing.	addCodonLine
Build Sets of Protein, Codon, Coding Nucleotide and Genomic Nucleotide Alignments for Specified Loci	alignmentFull
Search Alignments for Specific Positions in a Specific Allele	alignmentSearch
Allele Names Across All Release Versions	alleleListHistory
Trim All Versions of HLA Allele Names	alleleTrim
Generate a Complete set of Protein, Coding nucleotide and Genomic Nucleotide Atlases	atlasFull
Identify the Gene-Feature Boundaries in HLA Region Genes	atlasMaker
Stratify BIGDAWG Datasets by Specific Alleles	BDstrat
Convert BIGDAWG datasets to PyPop datasets Converts a BIGDAWG-formatted data frame into a pair of PyPop-formatted case and control data frames.	BDtoPyPop
Build Amino Acid, cDNA and gDNA Alignments	buildAlignments
Define Categories of Genes Supported by the IPD-IMGT/HLA Database	buildGazetteer
Generate a Table of Genomic Reference Alleles and Characteristics of HLA Genes Defined by the IPD-IMGT/HLA Database	buildGenomicReferences
Describe IPD-IMGT/HLA Database Genes, Identifying Pseudogenes and Gene Fragments	buildIMGTHLAGeneTypes
Ensure that AlignType Values are Valid	checkAlignType
Identify gDNA Alignments in Which the First Feature Boundary is not Identified as Position +1.	checkgDNAstart
Ensure that Source Values are Valid	checkSource
Check IPD-IMGT/HLA Release Version Allele Names	checkVersion
Identify Sequence Differences Between Two Alleles	compareSequences
Convert Values Across an Entire Data Frame or Vector	convertAny
Count the Spaces in a Character String	countSpaces
Generate a Customized Peptide, Codon or Nucleotide Sequence Alignment.	customAlign
Add 'Dot' Delimiters to a Numeric Release Version	expandVersion
Identify and Annotate Gene Features in Pseudogenes and Gene Fragments.	ffN
Format PyPop Data Frame Headers	formatHead
Gene Features of HLA Pseudogenes and Gene Fragments	fragmentFeatureNames
Retrieve Alignment Filenames for HLA Genes	getAlignmentNames
Trim Colon-Delimited HLA Allele Names by Field	getField
Identify the Latest IPD-IMGT/HLA Database Release	getLatestVersion
GL string code-Integrated Allele Name Translation	GIANT
Example Data Frame of Genotype List String Code Data	GLSC.ex
Translate GL String to UNIFORMAT	GLStoUNI
Example Data Frame of Genotype List String Data.	GLstring.ex
Translate GL Strings to UNIFORMAT Strings	GLtoUN
Update a GL String Code to a Specified IPD-IMGT/HLA Database Version	GLupdate
Retrieve Version from Input GL String	GLV
Format GL String Code Version Number	GLV2
Validate a GL String Code	GLvalidate
Locate Matches for an Incomplete IPD-IMGT/HLA Database Version	GLVhelper
Boundary Positions of Exons, Introns and UTRs in Amino Acid, cDNA and gDNA Alignments	HLAatlas
Functional and Organizational Categories of Genes Supported by the IPD-IMGT/HLA Database	HLAgazetteer
Genomic Reference Alleles for each Gene in the IPD-IMGT/HLA Database	IMGTGenomicReferences
Molecular characteristics of the Genes Curated by the IPD-IMGT/HLA Database	IMGTHLAGeneTypes
Identify Alleles that Share a Sequence Motif	motifMatch
Generate an Alignment for Specific Alleles at Different Positions	multiAlign
Trim Multiple HLA Allele Names	multiAlleleTrim
Translate Multiple GL Strings to UNIFORMAT	multiGLStoUNI
Apply validateLocus() to Multiple Loci	multiLocusValidation
Search Multiple Elements of Allele Names Across Release Versions	multiQueryRelease
Search Alignment Sequences at Multiple Positions for a Specified Allele	multiSearch
Translate a Vector of GL Strings to a Desired IPD-IMGT/HLA Database Version	multiTranslateGLstring
Translate Multiple UNIFORMAT Strings to GL Strings	multiUNItoGLS
Update a Vector of GL String Code Data to a Desired IPD-IMGT/HLA Database Version	multiUpdateGL
Identify the Number of Fields in a Colon-Delimited Allele Name	numFields
Guides for Parsing the Header Blocks of Alignment Files	parseAlignmentHead
Numerical Sort of Alignment Positions that Contain Indels	posSort
Convert BIGDAWG File Headers to PyPop Format	pypopHeaders
Extract Variant Information for Specific Positions in an Alignment	queryPositions
Search Allele Names Across Release Versions	queryRelease
Reintroduce Version Decimals	redec
Calculate Relative Risk for Individual Alleles and Genotypes in BIGDAWG-formatted Non-Case-Control Datasets	relRisk
Convert an AlleleListHistory Release Version to the GitHub Repository Version	repoVersion
Synthetic HLA Data for use with Package Examples	sHLAdata
Reduce a Release Version to Numerals	squashVersion
Translate HLA Allele Names across IPD-IMGT/HLA Database Release Versions	translateAllele
Translate a GL String across IPD-IMGT/HLA Database Release Versions	translateGLstring
Convert AlignType Values to Source Values	typeToSource
Generate an Alignment for Specific Alleles at Specific Positions	uniAlign
Example Data Frame of UNIFORMAT Data.	UNIFORMAT.example
Search Sequences at a Single Position for an Allele	uniSearch
Translate UNIFORMAT to GL String	UNItoGLS
Translate UNIFORMAT Strings to GL Strings	UNtoGL
Update All Package Data Objects Derived from IPD-IMGT/HLA Database Resources	updateAll
Build the AlleleList History R Object	updateAlleleListHistory
Update a GL String Code to a Specified IPD-IMGT/HLA Database Version	updateGL
Validate Allele-Name Format and Presence in HLAalignments	validateAllele
Validate a GL String	validateGLstring
Determine if a Locus Name is in the HLAgazetteer	validateLocus
Determine if a Motif is Properly Formatted	validateMotif
Validate the Presence of Variant Positions in an Alignment	validatePositions
Validate a UNIFORMAT String	validateUniformat
Validate an IPD-IMGT/HLA Release Version	validateVersion
Builds a Data Frame of Variant Information for Specific Positions in an Alignment	variantTable
Determine if an Allele Name Ever Existed, and (if so) in Which IPD-IMGT/HLA Database Releases	verifyAllele

Package: HLAtools 1.11.0

HLAtools: Toolkit for HLA Immunogenomics

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