isNamePresent

Checks if the name portion of the entered variant is present. Names consist of information following the locus and asterisk of the entered variant.

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

isNamePresent function

<dl><dt>variant</dt>
<dd>An amino acid motif or allele. Amino acid motifs must be in the following format: Locus*##$~##$~##$, where ## identifies a peptide position, and $ identifies an amino acid residue. Alleles must have 1-4 fields.</dd>
<dt>variantType</dt>
<dd>Identifies whether the variant is an allele or motif.</dd></dl>

Arguments

Checks if name portion of entered variant is present — isNamePresent

<dl>

<dt>variant</dt>
<dd>An amino acid motif or allele. Amino acid motifs must be in the following format: Locus*##$~##$~##$, where ## identifies a peptide position, and $ identifies an amino acid residue. Alleles must have 1-4 fields.</dd>


<dt>variantType</dt>
<dd>Identifies whether the variant is an allele or motif.</dd>

</dl>

isNamePresent: Checks if name portion of entered variant is present

Description

Usage

Value

Arguments