interactionEntry-class {Rintact}R Documentation

Class "interactionEntry"

Description

A class representing the interaction data extracted from an IntAct data file in PSI-MI 2.5 format.

Objects from the Class

Objects are usually created by psi25interaction.

Slots

releaseDate:
character, release date of the data entry, recorded in the entry element of the XML file.
organismName:
character, the unique organism name(s) of the interactors.
taxId:
character, the unique NCBI taxonomy ID(s) of the interactors.
interactors:
matrix, Each row represents one interactor. IntAct IDs are used as row names. Each column represents one annotation. Annotations include: UniProt ID, gene symbol, full name, locus name, ORF name, organism name, and NCBI taxonomy ID.
interactiones:
list, a list of intactInteraction objects, each represents one interaction.

Methods

show
signature(object = "interactionEntry"): a print method
bait
signature(object = "interactionEntry"): a method to find all the baits within the interactionEntry and print them
prey
signature(object = "interactionEntry"): a method to find all the prey within the interactionEntry and print them
interactions
signature(object = "interactionEntry"): a method to find all the interactions within the interactionEntry and print them
interactors
signature(object = "interactionEntry"): a method to find all the interactors within the interactionEntry and print them
organismName
signature(object = "interactionEntry"): a method to print all the unique organism names that are of the interactors
taxId
signature(object = "interactionEntry"): a method to print each taxonomy id for each organism
releaseDate
signature(object = "interactionEntry"): a method to print the updated release date of the PSI-MI 2.5 XML file; it serves as a proxy for versioning.

Author(s)

Nianhua Li

References

The IntAct Database: http://www.ebi.ac.uk/intact/site/contents/downloads.jsf.

See Also

intactInteraction-class, psi25interaction


[Package Rintact version 1.4.0 Index]