validateMotif {HLAtools}

Determine if a Motif is Properly Formatted

Description

Evaluates a motif to determine if the locus is valid and variants are valid.

Usage

validateMotif(motif, alignType)

Arguments

motif

A character string identifying a sequence variant motif in the following format: Locus*#$~#$~#$, where ## identifies a variant position, and $ identifies the sequence variant. Both nucleotide and peptide motifs can be provided, and any number of variants can be specified.

alignType

A character string identifying the type of alignment being searched. Allowed values are "codon","gen", nuc" and "prot". Only one 'alignType' value is allowed.

Value

If the motif is valid, TRUE is returned. If the locus or body of the motif is invalid, FALSE is returned along with a brief message.

Examples

validateMotif("A*-21M~2P","prot")
validateMotif("A*196G~301A~3046T","gen")