checkPosition {SSHAARP} | R Documentation |
Checks if amino acid positions in motif exist
Description
Checks if amino acid positions in the entered motif exist in IMGTprotalignments.
Usage
checkPosition(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. This function ONLY checks if the entered amino acid positions exist in IMGTprotalignments. |
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
TRUE if all of the amino acid positions in a motif exist. Otherwise, a vector with FALSE and an error message is returned.
Note
For internal SSHAARP use only.