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Filter to remove peptides from proteins failing the protein FDR threshold

filter_by_protein_fdr.Rd

This function filters the content of a summarised experiment based on a separate file detailing the proteins passing the FDR confidence threshold

This function is used to filter peptides to retain only those from proteins passing the FDR threshold

Usage

filter_by_protein_fdr(
  obj,
  protein_fdr_filename,
  protein_col_peptide = "Master.Protein.Accessions",
  protein_col_protein = "Accession",
  protein_FDR_col = "Protein.FDR.Confidence.Combined",
  retain_proteins = NULL
)

Arguments

obj

SummarisedExperiment containing peptide-level output from Proteome Discoverer.

protein_fdr_filename

string. Filepath for protein-level output from Proteome Discoverer

protein_col_peptide

string. Name of column containing master proteins in the peptide-level obj

protein_col_protein

string. Name of column containing master proteins in the protein-level protein_fdr_filename

protein_FDR_col

string. Name of column containing FDR information in the protein-level protein_fdr_filename

retain_proteins

character vector. Vector of protein accessions to always retain, even if they do not pass the FDR threshold. Default is NULL.

Value

Returns a SummarisedExperiment with the filtered Proteome Discoverer output.