Run PAnalyzer on Peptide-to-Protein Data

Executes the PAnalyzer tool on a provided peptide-to-protein dataset. This function writes the input data to a temporary file, runs the PAnalyzer tool using Java, and reads the output into R.

Usage

panalyzer(pep2prot)

Arguments

pep2prot

A data frame containing peptide-to-protein mappings. The data frame must include the columns peptideRef and proteinRef.

Value

A data frame with the original data and additional columns:

• peptideType: Type of the peptide determined by PAnalyzer. Possible values include "unique", "discriminating", and "non-discriminating".

• proteinType: Type of the protein determined by PAnalyzer. Possible values include "conclusive", "indistinguishable", "ambiguous", and "non-conclusive". All the proteins in a group will have the same proteinType value.

• groupRef: Group reference from PAnalyzer.

See also

• PAnalyzer: A software tool for protein inference in shotgun proteomics for more information on the tool.