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

In SSHAARP: Searching Shared HLA Amino Acid Residue Prevalence

Returns an alignment data frame of alleles that share a specific amino acid motif

Description

Returns an alignment data frame of alleles that share a specific amino acid motif.

Usage

findMotif(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.
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

An amino acid alignment dataframe of alleles that share the specified motif. Otherwise, a vector containing FALSE and an error message is returned.

Note

For internal SSHAARP use only.

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