Aggregate PSMs into Peptides

This function aggregates Peptide-to-Spectrum Matches (PSMs) into peptides, selecting the best PSM score for each peptide and maintaining decoy information. Peptides that are present in both the target and decoy subsets are removed from the final results.

Usage

iwf_psm2pep(psms, lower_better = TRUE)

Arguments

psms

A data.frame containing the PSM data, which must include columns peptideRef, psmScore, and isDecoy.

lower_better

A logical value indicating whether a lower PSM score is better. Default is TRUE.

Value

A data.frame containing one row per unique peptide with columns:

peptideRef

The peptide identifier.

pepScore

The best score for the peptide.

isDecoy

A logical indicating whether the peptide belongs to the decoy set.

See also

iwf_load_psms for loading PSMs.