psimi25InteractionEntry-class: Class "psimi25InteractionEntry"

Description Objects from the Class Slots Methods Author(s) See Also Examples

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 "list", a list of psimi25Interactor-class objects, each represents one interactor.

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

numInteractors

signature(x = "psimi25InteractionEntry"): returns the number of interactors.

numInteractions

signature(x = "psimi25InteractionEntry"): returns the number of interactions.

pubmedID

signature(x = "psimi25InteractionEntry"): returns the (unique) PubMed IDs of the papers reporting the interactions in the entry.

Author(s)

Tony Chiang <[email protected]> , Jitao David Zhang <[email protected]>

See Also

parsePsimi25Interaction, S4classpsimi25Interaction-class

Examples

1
showClass("psimi25InteractionEntry")

alyst/RpsiXML documentation built on July 10, 2017, 11:46 p.m.