MSMSpepXML-class: Class to contain MSMS peptide identification data.

In lgatto/RpepXML: R interface to the pepXML standard

Description

Class for the msms_pipeline_analysis element of the pepXML standard. This is the main object that will hold all the MSMS database search results.

Slots

pepFile:

Object of class "character" containing the name of the file used parsed to create the MSMSpepXML object.

searchEngine:

Object of class "character" describes the search engine used to generate data.

sampleEnzyme:

Object of class "character" described the enzyme used for sample digestion.

searchDatabase:

Object of class "character" describing the data base used for sepctra identification.

spectrumQueries:

Object of class "list" containing identification results for the queried MSMS sepctra. See also "SpectrumQuery".

.__classVersion__:

Object of class "Versions", documenting the version of the class.

Extends

Class "Versioned", directly.

Methods

filterHits

signature(object = "MSMSpepXML"): see filterHits-methods.

nProteins

signature(object = "MSMSpepXML"): see nProteins-methods.

nSearchHits

signature(object = "MSMSpepXML"): see nSearchHits-methods.

nSearchResults

signature(object = "MSMSpepXML"): see nSearchResults-methods.

pepFile<-

signature(object = "MSMSpepXML", value = "character"): see pepFile-methods.

pepFile

signature(object = "MSMSpepXML"): see pepFile-methods.

proteins

signature(object = "MSMSpepXML"): see proteins-methods.

sampleEnzyme<-

signature(object = "MSMSpepXML", value = "character"): see sampleEnzyme-methods.

sampleEnzyme

signature(object = "MSMSpepXML"): see sampleEnzyme-methods.

searchDatabase<-

signature(object = "MSMSpepXML", value = "character"): see searchDatabase-methods.

searchDatabase

signature(object = "MSMSpepXML"): see searchDatabase-methods.

searchEngine<-

signature(object = "MSMSpepXML", value = "character"): see searchEngine-methods.

searchEngine

signature(object = "MSMSpepXML"): see searchEngine-methods.

show

signature(object = "MSMSpepXML"): see show-methods.

spectrumQueries<-

signature(object = "MSMSpepXML", value = "list"): see spectrumQueries-methods.

spectrumQueries

signature(object = "MSMSpepXML"): see spectrumQueries-methods.

Author(s)

Laurent Gatto

See Also

parseMSMSpepXML, "SpectrumQuery", "SearchResult", "SearchHit"

Examples

showClass("MSMSpepXML")

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