Package: HLAtools 1.2.0

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.

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

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HLAtools.pdf |HLAtools.html✨
HLAtools/json (API)
NEWS

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

Peer review:

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

Datasets:
  • 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
  • HLAgazeteer - Functional and Organizational Categories of Genes Supported by the IPD-IMGT/HLA Database
  • IMGTHLAGeneTypes - Molecular characteristics of the Genes Curated by the IPD-IMGT/HLA Database
  • UNIFORMAT.example - Example Data Frame of UNIFORMAT Data.
  • alleleListHistory - Allele Names Across All Release Versions
  • fragmentFeatureNames - Gene Features of HLA Pseduogenes and Gene Fragments
  • sHLAdata - Synthetic HLA Data for use with Package Examples

On CRAN:

65 exports 1 stars 2.38 score 52 dependencies 7 scripts 785 downloads

Last updated 15 days agofrom:a166b52f27. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 02 2024
R-4.5-winOKSep 02 2024
R-4.5-linuxOKSep 02 2024
R-4.4-winOKSep 02 2024
R-4.4-macOKSep 03 2024
R-4.3-winOKSep 02 2024
R-4.3-macOKSep 02 2024

Exports:addCodonLinealignmentFullalignmentSearchalleleTrimatlasFullatlasMakerBDstratBDtoPyPopbuildAlignmentsbuildGazeteerbuildIMGTHLAGeneTypescheckAlignTypecheckgDNAstartcheckSourcecheckVersioncompareSequencesconvertAnycountSpacescustomAlignexpandVersionffNformatHeadgetAlignmentNamesgetFieldgetLatestVersionGIANTGLStoUNIGLtoUNGLupdateGLVGLV2GLvalidateGLVhelpermotifMatchmultiAlignmultiAlleleTrimmultiGLStoUNImultiLocusValidationmultiSearchmultiUNItoGLSmultiUpdateGLnumFieldsparseAlignmentHeadposSortpypopHeadersqueryReleaseredecrelRiskrepoVersionsquashVersiontypeToSourceuniAlignuniSearchUNItoGLSUNtoGLupdateAllupdateAlleleListHistoryupdateGLvalidateAllelevalidateGLstringvalidateLocusvalidateMotifvalidateUniformatvalidateVersionverifyAllele

Dependencies:askpassbootcellrangerclassclicpp11crayoncurldata.tableDescToolsdplyre1071ExactexpmfansifmsbgenericsgldgluehmshttrjsonlitelatticelifecyclelmommagrittrMASSMatrixmimemvtnormopensslpillarpkgconfigprettyunitsprogressproxyR6RcppreadxlrematchrlangrootSolverstudioapistringistringrsystibbletidyselectutf8vctrswithrxfun

HLAtools

Ryan Nickens -- [email protected], Livia Tran -- [email protected], Leamon Crooms IV -- [email protected], Derek Pappas, PhD -- [email protected], Vinh Luu -- [email protected], Josh Bredeweg, Steven J. Mack, PhD -- [email protected]

Rendered fromHLAtools.Rmdusingknitr::rmarkdownon Sep 02 2024.

Last update: 2024-08-20
Started: 2024-03-25

Readme and manuals

Help Manual

Help pageTopics
Add an 'AA codon' Line to Alignments When Missing.addCodonLine
Build Sets of Protein, Codon, Coding Nucleotide and Genomic Nucleotide Alignments for Specified LocialignmentFull
Search Alignments for Specific Positions in a Specific AllelealignmentSearch
Allele Names Across All Release VersionsalleleListHistory
Trim All Versions of HLA Allele NamesalleleTrim
Generate a Complete set of Protein, Coding nucleotide and Genomic Nucleotide AtlasesatlasFull
Identify the Gene-Feature Boundaries in HLA Region GenesatlasMaker
Stratify BIGDAWG Datasets by Specific AllelesBDstrat
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 AlignmentsbuildAlignments
Define Categories of Genes Supported by the IPD-IMGT/HLA DatabasebuildGazeteer
Describe IPD-IMGT/HLA Database Genes, Identifying Pseudogenes and Gene FragmentsbuildIMGTHLAGeneTypes
Ensure that AlignType Values are ValidcheckAlignType
Identify gDNA Alignments in Which the First Feature Boundary is not Identified as Position +1.checkgDNAstart
Ensure that Source Values are ValidcheckSource
Check IPD-IMGT/HLA Release Version Allele NamescheckVersion
Identify Sequence Differences Between Two Alleles at a LocuscompareSequences
Convert Values Across an Entire Data Frame or Vector Converts all instances of a value in a data frame or vector to a specified value.convertAny
Count the Spaces in a Character StringcountSpaces
Generate a Customized Peptide, Codon or Nucleotide Sequence Alignment.customAlign
Add 'Dot' Delimiters to a Numeric Release VersionexpandVersion
Identify and Annotate Gene Features in Pseudogenes and Gene Fragments.ffN
Format PyPop Data Frame Headers Format the header of a PyPop-formatted data frame.formatHead
Gene Features of HLA Pseduogenes and Gene FragmentsfragmentFeatureNames
Retrieve Alignment Filenames for HLA GenesgetAlignmentNames
Trim Colon-Delimited HLA Allele Names by FieldgetField
Identify the Latest IPD-IMGT/HLA Database ReleasegetLatestVersion
GLupdate-Integrated Allele Name TranslationGIANT
Example Data Frame of Genotype List String Code DataGLSC.ex
Translate GL String to UNIFORMATGLStoUNI
Example Data Frame of Genotype List String Data.GLstring.ex
Translate GL Strings to UNIFORMAT StringsGLtoUN
Update a GL String Code.GLupdate
Retrieve version from input GL String.GLV
Format GL String Code version number.GLV2
Validates 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 AlignmentsHLAatlas
Functional and Organizational Categories of Genes Supported by the IPD-IMGT/HLA DatabaseHLAgazeteer
Molecular characteristics of the Genes Curated by the IPD-IMGT/HLA DatabaseIMGTHLAGeneTypes
Identify Alleles that Share a Sequence MotifmotifMatch
Generate an Alignment for Specific Alleles at Different PositionsmultiAlign
Trim Multiple HLA Allele NamesmultiAlleleTrim
Translate Multiple GL Strings to UNIFORMATmultiGLStoUNI
Apply validateLocus() to Multiple LocimultiLocusValidation
Search Alignment Sequences at Multiple Positions for a Specified AllelemultiSearch
Translate Multiple UNIFORMAT Strings to GL StringsmultiUNItoGLS
Update a column of GL String Code data to a desired IPD-IMGT/HLA Database version.multiUpdateGL
Identify the Number of Fields in a Colon-Delimited Allele NamenumFields
Guides For Parsing the Header Blocks of Alignment FilesparseAlignmentHead
Numerical Sort of Alignment Positions that Contain IndelsposSort
Convert BIGDAWG File Headers to PyPop FormatpypopHeaders
Search Allele Names Across Release VersionsqueryRelease
Reintroduce version decimals.redec
Calculate Relative Risk for Individual Alleles and Genotypes in BIGDAWG-formatted Non-Case-Control DatasetsrelRisk
Convert an AlleleListHistory Release Version to the GitHub Repository VersionrepoVersion
Synthetic HLA Data for use with Package ExamplessHLAdata
Reduce a Release Version to NumeralssquashVersion
Convert AlignType Values to Source ValuestypeToSource
Generate an Alignment for Specific Alleles at Specific PositionsuniAlign
Example Data Frame of UNIFORMAT Data.UNIFORMAT.example
Search Sequences at a Single Position for an AlleleuniSearch
Translate UNIFORMAT to GL StringUNItoGLS
Translate UNIFORMAT Strings to GL StringsUNtoGL
Update All Package Data Objects Derived from IPD-IMGT/HLA Database ResourcesupdateAll
Build the AlleleList History R ObjectupdateAlleleListHistory
Update a GL String Code to a Specified IPD-IMGT/HLA Database Version.updateGL
Validate Allele-Name Format and Presence in HLAalignmentsvalidateAllele
Validate a GL StringvalidateGLstring
Determine if a Locus Name is in the HLAgazeteervalidateLocus
Determine if a Motif is Properly FormattedvalidateMotif
Validate a UNIFORMAT StringvalidateUniformat
Validate an IPD-IMGT/HLA Release VersionvalidateVersion
Determine if an Allele Name Ever Existed, and (if so) its Most Recent IPD-IMGT/HLA Database ReleaseverifyAllele