pepSequence-methods: Returns the sequence(s) of an identified peptide.

In lgatto/RpepXML: R interface to the pepXML standard

Description

This function returns and sets the sequence of the peptide(s) identified for one search hit or all the search hits of a search result. The output is a character of length equal to the number of search hits (when quering a search result) where each returned string has the format 'previous amino accid'.'peptide sequence'.'next amino acid'. A '-' represents the end of the protein sequence. 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 is returned.

signature(object = "SearchResult")

an object of class "SearchResult" is used as parameter and a character vector of length equal to the number of search hits is returned.

lgatto/RpepXML documentation built on May 21, 2019, 6:04 a.m.