add_site_sequence.Rd
Add a column with amino acid sequence around a PTM. Value will be
NA if peptide maps to multiple proteins or has multiple PTMs. If padding extends
outside the protein AA sequence, padding will be extended with '_'. The PTM-
centered AA sequence is useful to integrate external databases. Input
is PD output at PSM/peptide level having been passed through parse_PTM_scores
to add 'filtered_pos' column
add_site_sequence(
obj,
proteome_fasta,
master_protein_col = "Master.Protein.Accessions"
)
data.frame
with PD output at PSM/peptide level
character
Filepath for proteome fasta
character
Column name for master protein
data.frame