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

In SSHAARP: Searching Shared HLA Amino Acid Residue Prevalence

Verifies the alleles in entered haplotype are present in IMGTprotalignments

Description

Verifies the alleles in entered haplotype are present in IMGTprotalignments.

Usage

verifyAlleleANHIGHaplo(haplotype, filename, alignments)

Arguments

haplotype	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 "~".
filename	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.
alignments	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.

Value

TRUE if all alleles in a haplotype are present in the IMGTprotalignment object. Otherwise, a vector containing FALSE and an error message is returned.

Note

For internal SSHAARP use only.

SSHAARP documentation built on June 18, 2025, 1:08 a.m.