# Searching Shared HLA Amino Acid Residue Prevalence

## 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