checkPosition: Checks if amino acid positions in motif exist

In SSHAARP: Searching Shared HLA Amino Acid Residue Prevalence

Checks if amino acid positions in motif exist

Description

Checks if amino acid positions in the entered motif exist in IMGTprotalignments.

Usage

checkPosition(motif, filename, alignments)

Arguments

motif	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. This function ONLY checks if the entered amino acid positions exist in IMGTprotalignments.
filename	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.
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 of the amino acid positions in a motif exist. Otherwise, a vector with FALSE and an error message is returned.

Note

For internal SSHAARP use only.

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