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.
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
GLV                     Retrieve Version from Input GL String
GLV2                    Format GL String Code Version Number
GLVhelper               Locate Matches for an Incomplete IPD-IMGT/HLA
                        Database Version
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
GLvalidate              Validate a GL String Code
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
UNIFORMAT.example       Example Data Frame of UNIFORMAT Data.
UNItoGLS                Translate UNIFORMAT to GL String
UNtoGL                  Translate UNIFORMAT Strings to GL Strings
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
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
checkSource             Ensure that Source Values are Valid
checkVersion            Check IPD-IMGT/HLA Release Version Allele Names
checkgDNAstart          Identify gDNA Alignments in Which the First
                        Feature Boundary is not Identified as Position
                        +1.
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
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
uniSearch               Search Sequences at a Single Position for an
                        Allele
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
