Skip to contents

Assign Peptides to Protein Groups

iwf_pep2group.Rd

This function processes peptide-to-protein group relationships by summarizing the number of discriminating and total peptides per protein, and then assigning peptides to their respective protein groups. Proteins within a group are ordered by the number of discriminating peptides, followed by the total number of peptides.

Usage

iwf_pep2group(pep2prot2group, extra_pep_cols = c())

Arguments

pep2prot2group

A data frame containing peptide-to-protein-to-group relations. Must include at least peptideRef, proteinRef, groupRef, peptideType, and proteinType. It can also contain optional columns such as shared, isDecoy, pepScore, LP, or qval.

extra_pep_cols

A character vector of additional peptide-level column names to include in the summarization step (if present in the input data). These are combined with a default set of optional columns (shared, isDecoy, pepScore, LP, qval). Columns not present in the data are silently ignored.

Value

A data frame where peptides are assigned to protein groups. In addition to the original peptide and group identifiers, the result contains:

  • proteinCount: Number of proteins in each group.

  • proteinRefs: Concatenation of all protein references in the group.

  • proteinMaster: First protein of the group (after ordering).

  • Any optional peptide-level columns present in the input (e.g. shared, isDecoy, pepScore, LP, qval).

See also

iwf_grouping for generating peptide-to-protein-to-group relations, and panalyzer for protein grouping.