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]