scores-methods: Returns the peptide search scores.

In RpepXML: R interface to the pepXML standard

Description

This method returns and sets the search scores of a search hit. The scores will vary depending on the search engine used. The value is set automatically when creating an instance of "MSMSpepXML" with parseMSMSpepXML, and should generally not need to be changed. Mascot's ion score can individually be retrieved with ionScore-methods. When a search result is used, the scores of all the hits are returned.

Methods

signature(object = "SearchHit")

object of class "SearchHit" is given as parameter and a named numeric of length equal to the number of scores is returned.

signature(object = "SearchResult")

object of class "SearchResult" is given as paramter and a matrix is returned where the scores along the rows and the search hits along the columns.

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