psimi25InteractionEntry-class {RpsiXML}R Documentation

Class "psimi25InteractionEntry"

Description

A class representing interaction data parsed from PSI-MI 2.5 XML files

Objects from the Class

Objects can be created by calls of the form parsePsimi25Interaction

Slots

organismName:
Object of class "character", the unique organism name(s) of the interactors
taxId:
Object of class "character", the unique NCBI taxonomy ID(s) of the interactors
releaseDate:
Object of class "character", character, release date of the data entry, recorded in the entry element of the XML file
interactors:
Object of class "matrix", interactor information in a matrix, Each row represents one interactor. Source IDs are used as row names. Each column represents one annotation. Annotations include: UniProt ID, short label, organism name, and NCBI taxonomy ID
interactions:
Object of class "list", list, a list of psimi25Interaction-class objects, each represents one interaction.

Methods

interactions
signature(x = "psimi25InteractionEntry"): return a list of psimi25Intearaction objects, each representing one interaction
interactors
signature(x = "psimi25InteractionEntry"): a method to find all the interactors within the psimi25InteractionEntry and print them
organismName
signature(x = "psimi25InteractionEntry"): returns organism names of the interactors
releaseDate
signature(x = "psimi25InteractionEntry"): returns the release date, serving as a proxy for versioning
show
signature(object = "psimi25InteractionEntry"): a print method
taxId
signature(x = "psimi25InteractionEntry"): returns NCBI taxonomy ID

Author(s)

Tony Chiang <tchiang@ebi.ac.uk> , Jitao David Zhang <j.zhang@dkfz.de>

See Also

parsePsimi25Interaction, S4classpsimi25Interaction-class

Examples

showClass("psimi25InteractionEntry")

[Package RpsiXML version 1.0.0 Index]