Get the amino acid sequence around a PTM

Get the amino acid sequence around a PTM. Will return NA if peptide maps to multiple proteins or has multiple PTMs. If padding extends outside the protein AA sequence, padding will be extended with '_'.

get_sequence(proteome, protein, ptm_position, pad = 7)

Arguments

proteome

XStringSet as generated by Biostrings::readAAStringSet

protein

character protein ID

ptm_position

numeric position of the PTM in the protein

pad

numeric Number of amino acids around PTM

Value

character PSM-centered amino acid sequence