# Interface to EBI Intact protein interaction data base

## Documentation for package ‘Rintact’ version 1.0.0

## User Guides and Package Vignettes

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bait | A function that obtains the bait protein from the IntAct Interactions
bait,intactInteraction-method | Class "intactInteraction"
bait,interactionEntry-method | Class "interactionEntry"
complexEntry-class | Class "complexEntry"
complexes | A function that obtains the complex information from the IntAct Curated Protein Complexes
complexes,complexEntry-method | Class "complexEntry"
eListHandler | xmlEventParse handlers for MIF XML documents from EBI intact
iListHandler | xmlEventParse handlers for MIF XML documents from EBI intact
initialize,intactHyperGraph-method | Class "intactHyperGraph"
intactComplex-class | Class "intactComplex"
intactGraph-class | Class "intactGraph"
intactHyperGraph-class | Class "intactHyperGraph"
intactInteraction-class | Class "intactInteraction"
intactXML2Graph | A function that takes a vector of IntAct XML file names and converts them to graph objects.
interactionEntry-class | Class "interactionEntry"
interactions | A function that obtains the interaction information from the IntAct repository.
interactions,interactionEntry-method | Class "interactionEntry"
interactors | A function that obtains the interactors either in a binary interaction or a complex co-membership interaction.
interactors,complexEntry-method | Class "complexEntry"
interactors,interactionEntry-method | Class "interactionEntry"
list2Matrix | A function that takes a named list representation of a bipartite graph and transforms it into a matrix representation.
organismName | A method to obtain all the unique organism names from the PSI-MI 2.5 XML files upon which the data is based
organismName,interactionEntry-method | Class "interactionEntry"
prey | A function that obtains the prey protein from the IntAct Interactions
prey,intactInteraction-method | Class "intactInteraction"
prey,interactionEntry-method | Class "interactionEntry"
psi25complex | parser for PSI-MI 2.5 XML documents from EBI intact
psi25interaction | parser for PSI-MI 2.5 XML documents from EBI intact
releaseDate | A method to return the release date of the PSI-MI 2.5 XML file
releaseDate,interactionEntry-method | Class "interactionEntry"
show,complexEntry-method | Class "complexEntry"
show,intactComplex-method | Class "intactComplex"
show,intactGraph-method | Class "intactGraph"
show,intactHyperGraph-method | Class "intactHyperGraph"
show,intactInteraction-method | Class "intactInteraction"
show,interactionEntry-method | Class "interactionEntry"
taxId | A method to return all the unique taxonomy IDs indexing the unique organisms upon which the data is based
taxId,interactionEntry-method | Class "interactionEntry"
translateIntactID | A function that translates the IntAct accession codes for molecules to other common identifiers.
translateIntactID,intactGraph-method | Class "intactGraph"
translateIntactID,intactHyperGraph-method | Class "intactHyperGraph"