R: Toolkit for HLA Immunogenomics

# Toolkit for HLA Immunogenomics

## Documentation for package ‘HLAtools’ version 1.11.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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