findMotif

Returns an alignment data frame of alleles that share a specific amino acid motif.

Processes amino acid alignments produced by the 'IPD-IMGT/HLA (Immuno Polymorphism-ImMunoGeneTics/Human Leukocyte Antigen) Database' to identify user-defined amino acid residue motifs shared across HLA alleles, HLA alleles, or HLA haplotypes, and calculates frequencies based on HLA allele frequency data. 'SSHAARP' (Searching Shared HLA Amino Acid Residue Prevalence) uses 'Generic Mapping Tools (GMT)' software and the 'GMT' R package to generate global frequency heat maps that illustrate the distribution of each user-defined map around the globe. 'SSHAARP' analyzes the allele frequency data described by Solberg et al. (2008) <doi:10.1016/j.humimm.2008.05.001>, a global set of 497 population samples from 185 published datasets, representing 66,800 individuals total. Users may also specify their own datasets, but file conventions must follow the prebundled Solberg dataset, or the mock haplotype dataset.

Livia Tran

SSHAARP

Searching Shared HLA Amino Acid Residue Prevalence

Steven Mack

Josh Bredeweg

Dale Steinhardt

findMotif function

<dl><dt>motif</dt>
<dd>An amino acid motif in the following format: Locus*##$~##$~##$, where ## identifies a peptide position, and $ identifies an amino acid residue. Motifs can include any number of amino acids.</dd>
<dt>filename</dt>
<dd>The full file path of the user specified dataset if the user wishes to use their own file, or the pre-bundled Solberg dataset. User provided datasets must be a .dat, .txt, or.csv file, and must conform to the structure and format of the Solberg dataset.</dd>
<dt>alignments</dt>
<dd>A list object of sub-lists of data frames of protein alignments for the HLA and HLA-region genes supported in the ANHIG/IMGTHLA GitHub Repository. Alignments will always be the most recent version IPD-IMGT/HLA Database version.</dd></dl>

Arguments

Returns an alignment data frame of alleles that share a specific amino acid motif — findMotif

<dl>

<dt>motif</dt>
<dd>An amino acid motif in the following format: Locus*##$~##$~##$, where ## identifies a peptide position, and $ identifies an amino acid residue. Motifs can include any number of amino acids.</dd>


<dt>filename</dt>
<dd>The full file path of the user specified dataset if the user wishes to use their own file, or the pre-bundled Solberg dataset. User provided datasets must be a .dat, .txt, or.csv file, and must conform to the structure and format of the Solberg dataset.</dd>


<dt>alignments</dt>
<dd>A list object of sub-lists of data frames of protein alignments for the HLA and HLA-region genes supported in the ANHIG/IMGTHLA GitHub Repository. Alignments will always be the most recent version IPD-IMGT/HLA Database version.</dd>

</dl>

findMotif: Returns an alignment data frame of alleles that share a specific amino acid motif

Description

Usage

Value

Arguments