verifyAlleleANHIGHaplo

Verifies the alleles in entered haplotype are present in IMGTprotalignments.

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

verifyAlleleANHIGHaplo function

<dl><dt>haplotype</dt>
<dd>A haplotype where allele names are written in the IPD-IMGT/HLA Database format, and have 1-4 fields. Alleles in haplotypes must be delimited "~".</dd>
<dt>filename</dt>
<dd>The full file path of the user specified dataset if the user wishes to use their own file, or pre-bundled mock haplotype dataset. User provided datasets must be a .dat, .txt, or.csv file, and must conform to the structure and format of the mock haplotype dataset bundled with the package.</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

Verifies the alleles in entered haplotype are present in IMGTprotalignments — verifyAlleleANHIGHaplo

<dl>

<dt>haplotype</dt>
<dd>A haplotype where allele names are written in the IPD-IMGT/HLA Database format, and have 1-4 fields. Alleles in haplotypes must be delimited "~".</dd>


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

verifyAlleleANHIGHaplo: Verifies the alleles in entered haplotype are present in IMGTprotalignments

Description

Usage

Value

Arguments