findMotif: Returns an alignment data frame of alleles that share a...

In SSHAARP: Searching Shared HLA Amino Acid Residue Prevalence

Description

Consumes the alignment data frame produced by BLAASD() and returns an alignment data frame of alleles that share a specific amino acid motif.

Usage

findMotif(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

An amino acid alignment dataframe of alleles that share the specified motif. If the motif is not found in any alleles, or the motif has formatting errors, a warning message is returned.

Examples

#example with actual motif
findMotif("DRB1*26F~28E~30Y")
("DRB1*26F~28E")

#example with non-existent motif
findMotif("DRB1*26F~28E~30Z")

#extracting names of alleles with user-defined motif
findMotif("DRB1*26F~28E~30Y")[,4]

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