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Perform Protein Grouping Based on Peptide-to-Protein Relations

iwf_grouping.Rd

This function builds protein groups using the peptides that pass a specified peptide-level FDR threshold. Peptides that do not pass the threshold are grouped separately and assigned a negative group identifier. It utilizes the PAnalyzer algorithm to infer protein groups and assigns peptide and protein types.

Usage

iwf_grouping(pep2prot, threshold = 0.01)

Arguments

pep2prot

A data frame containing peptide-to-protein relations, including the columns peptideRef, proteinRef, qval, and isDecoy.

threshold

A numeric value specifying the peptide-level FDR threshold for grouping (default is 0.01).

Value

A data frame with the inferred protein groups, with additional columns:

  • peptideType: Type of peptide ("unique", "discriminating", "non-discriminating").

  • proteinType: Type of protein ("conclusive", "indistinguishable", "ambiguous", "non-conclusive").

  • groupRef: Group identifier for the proteins.

  • shared: The number of groups matched by each peptide.

See also

panalyzer for protein grouping, iwf_pep2level for obtaining peptide-to-protein relations.