get_sequence: Get the amino acid sequence around a PTM

In CambridgeCentreForProteomics/camprotR: Processing, analysing and visualising CCP proteomics data

Get the amino acid sequence around a PTM

Description

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

CambridgeCentreForProteomics/camprotR documentation built on July 7, 2024, 2:13 a.m.