checkMotifSyntax: Check motif syntax

In SSHAARP: Searching Shared HLA Amino Acid Residue Prevalence

Check motif syntax

Description

Checks if motif syntax is valid.

Usage

checkMotifSyntax(motif, filename)

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.
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.

Value

TRUE if the motif syntax is valid. Otherwise, a vector containing FALSE and an error message is returned.

Note

For internal SSHAARP use only.

Examples

#Example with correct motif syntax where user specified dataset is the Solberg dataset
checkMotifSyntax("DRB1*26F~28E~30Y", filename=SSHAARP::solberg_dataset)

#Example with incorrect motif syntax where user specified dataset is the Solberg dataset
checkMotifSyntax("DRB1****26F~28E", filename=SSHAARP::solberg_dataset)

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