add_PTM_positions: Add a column describing the position(s) of the PTM(s) with...

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

Add a column describing the position(s) of the PTM(s) with respect to the protein

Description

Identify the position(s) of the PTM(s) with respect to the protein. This is acheieved by finding the position of the peptide sequence in the protein and using the position(s) of the PTM(s) in the peptide sequence. Where a sequence has multiple master proteins or the position(s) of the PTM(s) are unknown, the position(s) of the PTM(s) with respect to the protein is undefined (NA). Input is PD output at PSM/peptide level having been passed through parse_PTM_scores to add 'filtered_pos' column

Usage

add_PTM_positions(
  obj,
  proteome_fasta,
  master_protein_col = "Master.Protein.Accessions",
  sequence_col = "Sequence"
)

Arguments

obj	data.frame with PD output at PSM/peptide level
proteome_fasta	string Filepath for proteome fasta
master_protein_col	string Name of column containing master protein IDs
sequence_col	string. Name of column containing peptide sequences

Value

data.frame

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