Description Usage Arguments Value Note Examples
Checks input motif for errors in format and amino acid positions not present in the locus alignment.
1 | checkMotif(motif)
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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. |
A warning message if the input motif is formatted incorrectly, or contains an amino acid position not present in the alignment. Otherwise, a list object with extracted locus information, a correctly formatted motif, and locus specific amino acid dataframe are returned. Note checkMotif() does not check amino acid variants in a specified motif; that is done by findMotif().
For internal SSHAARP use only.
1 2 3 4 5 6 7 8 | #Example where a motif is formatted correctly
checkMotif("DRB1*26F~28E~30Y")
#Example where format is incorrect
checkMotif("DRB1**26F~28E~30Y")
#Example where an amino acid position does not exist
checkMotif("DRB1**26F~28E~300000Y")
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