checkMotif: Syntactic and semantic validation of HLA amino acid motifs

In SSHAARP: Searching Shared HLA Amino Acid Residue Prevalence

Description

Checks input motif for errors in format and amino acid positions not present in the locus alignment.

Usage

checkMotif(motif)

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.

Value

A warning message if the input motif is formatted incorrectly, or contains an amino acid position not present in the alignment. Otherwise, a list object with extracted locus information, a correctly formatted motif, and locus specific amino acid dataframe are returned. Note checkMotif() does not check amino acid variants in a specified motif; that is done by findMotif().

Note

For internal SSHAARP use only.

Examples

#Example where a motif is formatted correctly
checkMotif("DRB1*26F~28E~30Y")

#Example where format is incorrect
checkMotif("DRB1**26F~28E~30Y")

#Example where an amino acid position does not exist
checkMotif("DRB1**26F~28E~300000Y")

SSHAARP documentation built on Sept. 17, 2021, 9:07 a.m.