Interface to EBI Intact protein interaction data base


[Package List] [Top]

Documentation for package ‘Rintact’ version 1.4.0

User Guides and Package Vignettes

Read overview or browse directory.

Help Pages

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"
separateXMLDataByExpt A function that takes a vector of IntAct XML file name locations and converts them to graph objects.
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"
translateNodeID A function that translates the IntAct accession IDs in an intactGraph to other common identifiers.
translateNodeID, intactGraph-method Class "intactGraph"
translateNodeID,intactGraph-method A function that translates the IntAct accession IDs in an intactGraph to other common identifiers.