HLAtools

Version 1.3.0

• November 11, 2024
• HLAatlas, HLAgazeteer, alleleListHistory and fragmentFeatureNames updated to IPD-IMGT/HLA Database release 3.58.0.
• Exported HLAgazeteer for use in validateLocus(), multiLocusValidation(), and buildAlignments().
• Updated buildAlignments() to append expression suffixes to the truncated names of 3- and 4-field alleles with expression variant suffixes.
• Added multiQueryRelase(), extending queryRelease() to search for multiple allele-name elements.
• Updated the package vignette.
• Spelling corrections in fragmentFeatureNames documentation.

Version 1.2.0

• August 20, 2024
• Added multiAlleleTrim() for trimming vectors of allele names in a single nomenclature epoch.

Version 1.1.4

• August 16, 2024
• Revised multiUpdateGL() to avoid collisions between allele names and version identifiers, improve messaging and efficiency, update sets of GL String Codes generated under different release versions, and append “HLA-” to allele names in returned GLSCs.
• Changed release version in GLSC.ex dataset from 3.1.0 to 3.01.0.
• Updated alleleTrim() to optionally include expression variants in truncated allele names.

Version 1.1.3

• August 2, 2024
• Package version 1.1.1 published on CRAN Repository on July 26, 2024.
• Updated the feature names for HLA-R in fragmentFeatureNames.
• Described all four non-standardard features in ffN() documentation.
• Minor corrections to vignette.
• Updated package Description.

Version 1.1.2

• July 24 to July 25, 2024
• Updated the bundled HLAatlas object to include non-standard features for the HLA-R gDNA atlas.
• Changed the date on the IMGTHLAGeneTypes object from “09-07-2024” to “08-07-2024” to reflect the date on the updated hla.alleles.org/genes/index.html page.
• Corrected a typo in documentation for ffn().
• Updated atlasMaker() to return non-standard gene feature names for the HLA-R, -S, -T, -V, and -W cDNA atlases.
• Noted non-standard features in HLAatlas and atlasMaker documentation.
• Updated data/HLAatlas.rda file to reflect these changes.

Version 1.1.1

• July 21, 2024
• Added link to ANHIG/IMGTHLA GitHub repo in Description.
• Removed example from BuildIMGTHLAGeneTypes().
• Modified updateAll() to load new objects into the parent.frame() environment, rather than .GlobalEnv.
• Submission to CRAN.

Version 1.1.0

• July 17, 2024
• Added the GIANT() function for translating vectors and data frames of HLA allele names across IPD-IMGT/HLA Database release versions.
• Updates to ReadMe and Vignette.
• Updates to function examples.
• Submission to CRAN.

Version 1.0.4

• July 12, 2024
• Modified functions to support and incorporate the new HLA-R gene.
• Corrected fragmentFeaturesNames annotations for HLA-P and -W.
• Updated the alleleListHistory, fragmentFeatureNames, HLAgazeteer and HLAatlas data objects to version 3.57.0, and IMGTHLAGeneTypes to version 09-07-2024, and aded these versions to the package.

Version 1.0.3

• July 10, 2024
• Corrected typo in queryRelease() documentation.
• Expanded acronyms in DESCRIPTION.
• Added ‘value’ lines to addCodonLine(), getField(), typeToSource() and updateAll().
• Minor edits to other function descriptions.
• Replaced ‘dontrun’ with ‘donttest’ in function documentations, or remove ‘dontrun’ in some cases.
• Removed note for atlasFull().
• Removed pseudo.codon global variable and zzz.R file.
• Updated GLVhelper() for full release versions 1., 2. and 3.* functionality.
• Streamlined updateGL() functionality and include informative examples.
• Updated documentation and examples for GLupdate(), GLV(), GLV2, redec().
• Updated GLVhelper() functoinality, documention and messaging.
• Added ‘namespace’ parameter to GLvalidate(), supporting HLA and KIR GLSC namespaces, although KIR is not supported in the HLAtools package.
• Added BIGDAWG-formatted sHLAdata synthetic dataset for use with BDstrat(), BDtoPyPop() and relRisk().
• Added calls to sHLAdata in BDstrat(), BDtoPyPop() and relRisk() examples.
• Updated ReadMe and Vignette.

Version 1.0.2

• June 28, 2024
• Removed GPL license document.
• Adopted canonical URL to BIGDAWG input format in relRisk() and BDStrat().
• Added URL to HLAtools GitHub repository.
• Correct titles for ExpandVersion() and GLtoUN() functions.
• Submission to CRAN.

Version 1.0.1

• June 27, 2024
• Wrapped individual authors in c() in DESCRIPTION.
• Limited ‘cre’ role to the package Maintainer.
• Submission to CRAN.

Version 1.0.0

• June 26, 2024
• Standardized function documentation.
• Remove write.table() calls from atlasMaker().
• Add save.path parameter to BDtoPyPop() and relRisk().
• initial package release.
• Submission to CRAN.

Version 0.9.16.9000 June 24th to 25th, 2024

• Updated atlasMaker() to build atlases for DRB1 in release 3.48.0.
• Updated atlasMaker() to build atlases for HLA-B in releases 3.44.0 and 3.43.0.
• Updated atlasMaker() to build atlases for HFE in releases 3.27.0 to 3.22.0.
• Updated atlasMaker() to build atlases for HLA-V in release 3.14.0.
• Updated atlasMaker() to build atlases for DPA2 and DPB2 in releases 3.53.0-3.27.0.
• Updated atlasMaker() to build atlases for HLA-N, -S, -U, and -Y in releases 3.35.0-3.33.0.
• Updated atlasMaker() to build atlases for HLA-Y in releases 3.32.0-3.20.0.
• Updated atlasMaker() to build atlases for HLA-W and -T in release 3.27.0.
• Updated atlasMaker() to build atlases for All loci in release 3.13.0/3.13.1.
• Updated atlasMaker() to build atlases for HLA-C in release 3.02.0.
• Updated atlasMaker() to build atlases for DPA, DPB, TAP1 and TAP2 in release 3.00.0.
• Stopped atlasMaker() writing correspondence_tables to tempdir.

Version 0.9.15.9000 June 21, 2024

• Added addCodonLine() function to facilitate fixing nucleotide alignments that are missing “AA codon” lines.

Version 0.9.14.9000 June 10th to 20th, 2024

• Updated buildAlignments() to build DPA2 and DPB2 cDNA alignments in releases prior to 3.54.0.
• Updated buildAlignments() to build DRB1 gDNA alignments in release 3.48.0.
• Updated buildAlignments() to build HLA-B cDNA alignments in releases 3.44.0 and 3.43.0.
• Updated buildAlignments() to build HLA-N, -S, -U and -Y cDNA alignments in releases prior to 3.36.0.
• Updated buildAlignments() to build HLA-W and -T cDNA alignments in release 3.27.0.
• Updated buildAlignments() to build HFE cDNA alignments in releases prior to 3.28.0.
• Updated buildAlignments() to build HLA-DPA, -DPB, -DQA and -DQB AA alignments in releases prior to 3.24.0. The returned objects are “\(DPA", "\)DPB”, “\(DQA" and "\)DQB”, the loci in these objects are “DPA1”, “DPB1”, “DQA1” and “DQB1”.
• Updated buildAlignments() to build HLA-V in version 3.14.0.
• Updated buildAlignments() to account for version inconsistency (3.13.0 vs 3.13.1) in release 3.13.1 alignments.
• Updated documentation of repoVersion() for accuracy.
• Applied repoVersion() in buildAlignments().
• Modified buildGazeteer() to account for version differences in URL and alignment files for release 3.13.0/3.13.1.
• Updated buildAlignments() to build HLA-C cDNA alignments in release 3.02.0.
• Close connections in HLAgazeteer().
• Updated buildAligmments() to build HLA-DOA AA alignment in release 3.01.0.
• Updated documentation for updateAll().
• Updated repoVersion() for release 3.00.0.
• Updated buildAlignments() to build HLA-DPA and -DPB cDA alignments in release 3.00.0.
• Updated buildAlignments() to build TAP1 and TAP2 cDNA alignments in version 3.00.0.

Version 0.9.13.9000 June 4, 2024

• Clarified that the oldest available release for GL String Code updating is version 1.05.0.
• Changed the default IMGT/HLA Release version for alignmentFull() to the version of the loaded HLAgazeteer.

Version 0.9.12.9000 May 28, 2024

• Added motifMatch() and validateMotif() functions. Thanks to Kazu Osoegawa for the suggestion.
• Updated documentation for checkAlignType().
• Corrected documentation for fragmentFeatureNames.

Version 0.9.11.9000 May 16, 2024

• Updated package title.
• Minor updates to Vignette.
• Changed ’*’ to ‘#’ for PyPop version references.
• Complete citations for published sources of the HLAgazeteer.
• Limited asterisks in function parameter documentation.
• Added link to PyPop configuration file webpage in pypopHeaders().
• Added locus sanity check in compareSequences().
• Modified getField() so that NA values are not appended to an allele name when a resolution higher than that of the provided allele is requested.

Version 0.9.10.9000 May 10, 2024

• Updated buildGazeteer() to account for the DRB2, DRB6, DRB7 and DRB9 gene.
• Updated documentation for HLAgazeteer regarding the DRB2, DRB6, DRB7 and DRB9 genes and the DRB alignment files.
• Updated documentation for fragmentFeatureNames() regarding the DRB2, DRB6, DRB7 and DRB9 genes and genomic alignments.
• Updated the vignette to reflect these issues.

Version 0.9.9.9000 May 3, 2024

• Added BDtoPyPop() function.
• Updates to Vignette, ReadMe and Description.

Version 0.9.8.9000 April 27, 2024

• Removed reliance on HTexceptions data object.
• Correction to relRisk().

Version 0.9.7.9000 April 20, 2024

• Standardized use of ‘source’ in documentation.
• Changed ‘alignType’ parameter to ‘source’ in multiLocusValidation().
• Added checkAlignType() and checkSource() functions for converting between alignmentType (for alignment objects) and source (for alignment files) values.
• Added checkAlignType() to AlignmentFull().
• Suppressed warning messages in alignmentFull() and atlasMaker().
• Restricted compareSequences() to a single ‘alignType’.
• Clarified when only a single ‘alignType’ is allowed for a function.
• Edits to Vignette.

Version 0.9.6.9000 April 15, 2024

• Added the queryRelease() function for searching the alleleListHistory object.
• Formalized and streamlined the GL String to UNIFORMAT and UNIFORMAT to GL String functions and updated documentation.
• Corrected documentation for customAlign().
• Corrected Markdown formatting in BDstrat.R.
• First draft of complete Vignette.

Version 0.9.5.9000 April 11, 2024

• Added ‘source’ selection to multiLocusValidation().
• Modified atlasMaker() to support updated multiLocusValidation().
• Updated packaged data objects (HLAatlas,HLAgazeteer,fragmentFeatureNames and alleleListHistory) to version IPD-IMGT/HLA Database Release version 3.56.0.
• Updated Vignette.

Version 0.9.4.9000 April 9, 2024

• Added HTexceptions() and the HTexceptions data object, which make defined exceptions for specific use cases available for package functions.
• Added HTexceptions.rda to the /data folder.
• Updated atlasMaker() to use HTexceptions for building DPA2, DPB2 and HLA-Y nucleotide atlases.
• Updated atlasMaker() to use multiLocusValidation(), which depends on the HLAgazeteer$version to evaluate locus:version matches.
• Modified multiLocusValidation() messaging to reflect this dependence on HLAgazeteer$version.
• Updates to Vignette.
• Updates to ReadMe.

Version 0.9.3.9000 April 7, 2024

• Correctly added GPL3 License to package.
• Added getAlignmentNames() function.
• Added repoVersion() function.
• Added parseAlignmentHead() function.
• Updated buildGazeteer() to use getAlignmentNames().
• Updated atlasMaker(), buildAlignments() and buildGazeteer() to use repoVersion().
• Updates to Vignette.
• Updates to ReadMe.

Version 0.9.2.9000 April 3, 2024

• Added multiLocusValidation() function.
• Applied multiLocusValidation() in AlignmentFull().
• Closed connections in versionValidation().
• Added documentation to fragmentFeatureNames.R.
• Added content to Vignette.
• Corrected returned list names in BDstrat().
• Updated ReadMe.
• Updated documentation for relRisk().

Version 0.9.1.9000 April 1, 2024

• Minor update to alignmentFull().
• Updated alignmentFull() documentation to note the absence of DP and DQ gene numbers in older database releases.
• Added sections to Vignette.
• Reformatted News to include bullets.

Version 0.9.0.9000 March 31, 2024

• Updated BDStrat() to function on multiple alleles at multiple loci.
• Added sections to Vignette.

Version 0.8.1.9000 March 24, 2024

• Added the BDstrat() function for stratifying BIGDAWG-formatted datasets by single alleles
• Added the verifyAllele() function, which leverages AlleleListHistory to determine if and when a full alllele name was valid.
• Updated ReadMe.

Version 0.8.0.9000 March 21, 2024

• Added the relRisk() function for calculating relative risk using BIGDAWG-formatted datasets.
• Added $align to HLAgazeteer to identify all genes with alignments.
• Added new versions of the HLAatlas, HLAgazeteerm IMGTHLAGeneTypes, alleleListHistory, and fragmentFeatureNames objects to the package.
• Updated ReadMe.
• Added bullet points to News.

Version 0.7.7.9000 March 19, 2024

• Updated posSort() and and alignmentSearch() to address edge-cases and support searching for intron positions.
• Updated getField() so that expression variant identifiers are optionally appended to truncated versions of full-length expression variants.
• Reestructured descriptions of several functions for clarity.

Version 0.7.6.9000 March 19, 2024

• Standardized versioning for the packaged data objects.
  
• Added functionality for updating packaged data objects.

Version 0.7.5.9000 March 13, 2024

• Expanded HLAgazeteer to define multiple functional and organizational sets of genes.
  
• Expanded alignmentFull() to build user-defined sets of alignments.
  
• Updated ReadMe and Description to reflect expanded capacities.

Version 0.7.4.9000 February 18, 2024

• Consolidated sequence query and custom alignment building functions to support all alignments.

Version 0.7.3.9000 February 16, 2024

• Added a nucleotide (‘nuc’) aligmment to HLAalignments, and changed the previous ‘nuc’ alignment to ‘codon’.
  
• Nucleotide sequence query functions support both nucleotide and codon cDNA aligmnents.

Version 0.7.2.9000 February 10, 2024

• Added documentation, updated functions for building alignments.

Version 0.7.1.9000 February 9, 2024

• HLAtools Package contains reference datasets, along side query and analysis tools.