psimi25Interaction-class: Class "psimi25Interaction"

In alyst/RpsiXML: R interface to PSI-MI 2.5 files

Description

A class representing interaction data

Objects from the Class

Objects can be created by calls of the form parsePsimi25Interaction

Slots

sourceDb:

Object of class "character", source database

sourceId:

Object of class "character", source database ID

interactionType:

Object of class "character", character, the method used for detecting the interaction ,such as "pull down"

expPubMed:

Object of class "character", PubMed ID of the publication that describes the experiment

sourceId:

Object of class "character", source database ID of the experiment

confidenceValue:

Object of class "character", confidence value of the experimental interaction

participant:

Object of class "character", UniProt IDs of the participants. Important when no bait/prey information is available

bait:

Object of class "character", UniProt ID of the bait

prey:

Object of class "character", UniProt ID(s) of the prey(s)

inhibitor:

Object of class "character", UniProt ID of the inhibitor, NA when missing

neutralComponent:

Object of class "character", UniProt ID of the neutral components, NA when missing

baitUniProt:

An object of class "character"

preyUniProt:

An object of class "character"

Methods

interactionType

signature(x = "psimi25Interaction"): finds out interaction type

show

signature(object = "psimi25Interaction"): a print method

sourceDb

signature(x = "psimi25Interaction"): finds out source database

sourceId

signature(x = "psimi25Interaction"): returns ID of the source database

bait

signature(x = "psimi25Interaction"): returns the UniProt ID of the bait

prey

signature(x = "psimi25Interaction"): returns the UniProt ID(s) of the prey(s)

confidenceValue

signature(x = "psimi25Interaction"): returns the confidence value of the interaction

Author(s)

Tony Chiang <[e-mail]> , Jitao David Zhang <[e-mail]>

See Also

parsePsimi25Interaction,S4CLASSpsimi25Interactor-class, S4CLASSpsimi25Experiment-class, S4classpsimi25InteractionEntry-class

Examples

showClass("psimi25Interaction")

alyst/RpsiXML documentation built on Nov. 21, 2019, 5:47 a.m.