adjustProteinAssignments: Add missing proteins to PSM-level data based on a fasta...

In Vitek-Lab/SharedPeptidesExplorer: Weighted Protein-Level Summarization for Protein Clusters

Add missing proteins to PSM-level data based on a fasta database

Description

Add missing proteins to PSM-level data based on a fasta database

Usage

adjustProteinAssignments(
  quantification_data,
  fasta_db_path,
  protein_column = "ProteinName",
  peptide_column = "PeptideSequence",
  n_cores = 1,
  keep_unmodified = FALSE
)

Arguments

quantification_data	MS data, preferably in 'MSstats' or 'MSstatsTMT' format.
fasta_db_path	path to a fasta file that store protein sequences
protein_column	name of a column with protein names.
peptide_column	name of a column with peptide sequences.
n_cores	number of cores that will be used while searching the database.
keep_unmodified	if TRUE, a column that stores sequences of unmodified peptides will be added to output data

Vitek-Lab/SharedPeptidesExplorer documentation built on April 14, 2025, 1:45 p.m.