findMotif {SSHAARP} | R Documentation |
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.