Searching Shared HLA Amino Acid Residue Prevalence

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Documentation for package ‘SSHAARP’ version 2.0.8

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

Help Pages

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