Toolkit for HLA Immunogenomics

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Documentation for package ‘HLAtools’ version 1.1.1

• 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 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
buildGazeteer	Define Categories of Genes Supported 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 at a Locus
convertAny	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.
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 Format the header of a PyPop-formatted data frame.
fragmentFeatureNames	Gene Features of HLA Pseduogenes 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	GLupdate-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.
GLV	Retrieve version from input GL String.
GLV2	Format GL String Code version number.
GLvalidate	Validates 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
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
motifMatch	Identify Alleles that Share a Sequence Motif
multiAlign	Generate an Alignment for Specific Alleles at Different Positions
multiGLStoUNI	Translate Multiple GL Strings to UNIFORMAT
multiLocusValidation	Apply validateLocus() to Multiple Loci
multiSearch	Search Alignment Sequences at Multiple Positions for a Specified Allele
multiUNItoGLS	Translate Multiple UNIFORMAT Strings to GL Strings
multiUpdateGL	Update columns 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
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
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 HLAgazeteer
validateMotif	Determine if a Motif is Properly Formatted
validateUniformat	Validate a UNIFORMAT String
validateVersion	Validate an IPD-IMGT/HLA Release Version
verifyAllele	Determine if an Allele Name Ever Existed, and (if so) its Most Recent IPD-IMGT/HLA Database Release