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 |
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 |
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 |
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 |
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 |
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 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) in Which IPD-IMGT/HLA Database Releases |