proteins-methods: Returns the proteins associated with identifies peptides.

In RpepXML: R interface to the pepXML standard

Description

This method returns and sets the protein identifiers for individual search hits. The values are set automatically when creating an instance of "MSMSpepXML" with parseMSMSpepXML, and should generally not need to be changed.

Methods

signature(object = "SearchHit")

an object of class "SearchHit" is used as parameter and a character vector of possibly multiple proteins is returned.

signature(object = "SearchResult")

an object of class "SearchResult" is used as parameter and a character vector of all possibly alternative proteins for the search hits is returned.

signature(object = "SpectrumQuery")

an object of class "SpectrumQuery" is used as parameter and a character vector of all possibly alternative proteins for the search results is returned.

signature(object = "MSMSpepXML")

an object of class "MSMSpepXML" is used as parameter and a list of characters of length equal to the number of spectrum queries is returned.

RpepXML documentation built on May 2, 2019, 5:15 p.m.