add_site_sequence: Add a column with amino acid sequence around a PTM

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

Add a column with amino acid sequence around a PTM

Description

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

Usage

add_site_sequence(
  obj,
  proteome_fasta,
  master_protein_col = "Master.Protein.Accessions"
)

Arguments

obj	data.frame with PD output at PSM/peptide level
proteome_fasta	character Filepath for proteome fasta
master_protein_col	character Column name for master protein

Value

data.frame

CambridgeCentreForProteomics/camprotR documentation built on Jan. 27, 2023, 8:36 p.m.