Get the amino acid sequence around a PTM — get

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 '_'.

Usage

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