Searching Shared HLA Amino Acid Residue Prevalence


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Documentation for package ‘SSHAARP’ version 2.0.8

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checkAlleleSyntax Check allele syntax
checkHaplotypeSyntax Check haplotype syntax
checkLocusDataset Check locus validity and if the locus is present in the user specified dataset
checkMotifSyntax Check motif syntax
checkPosition Checks if amino acid positions in motif exist
dataSubset Dataset manipulation for motifs and alleles
dataSubsetHaplo Dataset manipulation for haplotypes
findMotif Returns an alignment data frame of alleles that share a specific amino acid motif
getVariantInfo Locus and allele or motif extraction for motifs, allele, or haplotype mapping
isNamePresent Checks if name portion of entered variant is present
mock_haplotype_dataset Mock Haplotype Dataset
PALM Population Allele Locating Mapmaker
readFilename Designates dataset by either reading in file the user has provided, or using the Solberg dataset or mock haplotype dataset
solberg_dataset Solberg Dataset
validateVariantType validateVariantType
verifyAlleleANHIG Verifies the allele entered is present in the IMGT protein alignments
verifyAlleleANHIGHaplo Verifies the alleles in entered haplotype are present in IMGTprotalignments
verifyAlleleDataset Verifies the allele entered is present in specified dataset