Entry: BIOGRID.PSIMI25
Aliases: BIOGRID.PSIMI25 DIP.PSIMI25 HPRD.PSIMI25 INTACT.PSIMI25 MINT.PSIMI25 MIPS.PSIMI25 MATRIXDB.PSIMI25 CORUM.PSIMI25 MPACT.PSIMI25
Keywords: models
Description: Supported PSI-MI 2.5 XML data sources
URL: ../../../library/RpsiXML/html/BIOGRID.PSIMI25.html

Entry: availableXrefs-methods
Aliases: availableXrefs-methods availableXrefs,list-method availableXrefs,psimi25InteractionEntry-method availableXrefs,psimi25Interactor-method
Keywords: methods models
Description: Methods for function availableXrefs
URL: ../../../library/RpsiXML/html/availableXrefs-methods.html

Entry: availableXrefs
Aliases: availableXrefs xref
Keywords: models
Description: Get cross reference(s) of interactors from PSI-MI 2.5 files
URL: ../../../library/RpsiXML/html/availableXrefs.html

Entry: bait
Aliases: bait prey participant inhibitor pubmedID confidenceValue neutralComponent
Keywords: models
Description: Extract bait, prey, participant, inhibitor, pubmed, confidence value, interaction type, or neutral component information from an object of psimi25Interaction-class
URL: ../../../library/RpsiXML/html/bait.html

Entry: buildPCHypergraph
Aliases: buildPCHypergraph
Keywords: 
Description: Build protein complex hypergraph from PSI-MI 2.5 files
URL: ../../../library/RpsiXML/html/buildPCHypergraph.html

Entry: complexName
Aliases: complexName complexMembers complexAttributes
Keywords: models
Description: Accessor functions for complex
URL: ../../../library/RpsiXML/html/complexName.html

Entry: complexes
Aliases: complexes
Keywords: models
Description: Extract complexes from psimi25ComplexEntry
URL: ../../../library/RpsiXML/html/complexes.html

Entry: eListHandler
Aliases: eListHandler iListHandler
Keywords: models
Description: xmlEventParse handlers for PSI-MI XML documents
URL: ../../../library/RpsiXML/html/eListHandler.html

Entry: getAbstractByPMID
Aliases: getAbstractByPMID
Keywords: models
Description: A function to obtain the abstract information via a Pubmed ID
URL: ../../../library/RpsiXML/html/getAbstractByPMID.html

Entry: graphConverter
Aliases: graphConverter hyperGraphConverter
Keywords: manip
Description: maps one type of grap onto another
URL: ../../../library/RpsiXML/html/graphSpeciesConverter.html

Entry: interactionType
Aliases: interactionType
Keywords: models
Description: Type of the interaction
URL: ../../../library/RpsiXML/html/interactionType.html

Entry: interactions
Aliases: interactions
Keywords: models
Description: List interactions in the given psimi25InteractionEntry object
URL: ../../../library/RpsiXML/html/interactions.html

Entry: interactorInfo-methods
Aliases: interactorInfo-methods interactorInfo,list-method interactorInfo,psimi25ComplexEntry-method interactorInfo,psimi25Graph-method interactorInfo,psimi25InteractionEntry-method
Keywords: methods
Description: Methods for Function interactorInfo in Package 'RpsiXML'
URL: ../../../library/RpsiXML/html/interactorInfo-methods.html

Entry: interactorInfo
Aliases: interactorInfo
Keywords: models
Description: Interactor info in a matrix
URL: ../../../library/RpsiXML/html/interactorInfo.html

Entry: interactors-methods
Aliases: interactors-methods interactors,psimi25Graph-method interactors,psimi25Hypergraph-method
Keywords: methods
Description: Methods for Function interactors
URL: ../../../library/RpsiXML/html/interactors-methods.html

Entry: interactors
Aliases: interactors
Keywords: models
Description: Interactors of the given object
URL: ../../../library/RpsiXML/html/interactors.html

Entry: list2Matrix
Aliases: list2Matrix
Keywords: models
Description: Converts list into matrix
URL: ../../../library/RpsiXML/html/list2Matrix.html

Entry: null2na
Aliases: null2na
Keywords: models
Description: Turns null or NA into character "NA"
URL: ../../../library/RpsiXML/html/null2na.html

Entry: numInteractions-methods
Aliases: numInteractions numInteractions-methods numInteractions,psimi25InteractionEntry-method
Keywords: methods
Description: Get interaction number of the given object
URL: ../../../library/RpsiXML/html/numInteractions-methods.html

Entry: numInteractors-methods
Aliases: numInteractors numInteractors-methods numInteractors,psimi25Hypergraph-method numInteractors,psimi25InteractionEntry-method
Keywords: methods
Description: Get interactor number of the given item
URL: ../../../library/RpsiXML/html/numInteractors-methods.html

Entry: organismName-methods
Aliases: organismName organismName-methods organismName,psimi25Complex-method organismName,psimi25Interactor-method
Keywords: methods
Description: Returns the organism name(s) of the given item
URL: ../../../library/RpsiXML/html/organismName-methods.html

Entry: parseComplex
Aliases: parseComplex parseInteractor parseExperiment
Keywords: models
Description: Parse complex, interactor and experiment from PSI-MI 2.5 XML node
URL: ../../../library/RpsiXML/html/parseComplex.html

Entry: parsePsimi25Interaction
Aliases: parsePsimi25Interaction parsePsimi25Complex
Keywords: models
Description: Parsing PSI-MI 2.5 XML documents into interactions
URL: ../../../library/RpsiXML/html/parsePsimi25Interaction.html

Entry: psimi25Complex-class
Aliases: psimi25Complex-class show,psimi25Complex-method complexAttributes,psimi25Complex-method complexMembers,psimi25Complex-method complexName,psimi25Complex-method
Keywords: classes
Description: Class "psimi25Complex"
URL: ../../../library/RpsiXML/html/psimi25Complex-class.html

Entry: psimi25ComplexEntry-class
Aliases: psimi25ComplexEntry-class complexes,psimi25ComplexEntry-method interactors,psimi25ComplexEntry-method show,psimi25ComplexEntry-method
Keywords: classes
Description: Class "psimi25ComplexEntry"
URL: ../../../library/RpsiXML/html/psimi25ComplexEntry-class.html

Entry: psimi25Experiment-class
Aliases: psimi25Experiment-class
Keywords: classes
Description: Class "psimi25Experiment"
URL: ../../../library/RpsiXML/html/psimi25Experiment-class.html

Entry: psimi25Graph-class
Aliases: psimi25Graph-class show,psimi25Graph-method abstract,psimi25Graph-method
Keywords: classes
Description: Class "psimi25Graph" ~~~
URL: ../../../library/RpsiXML/html/psimi25Graph-class.html

Entry: psimi25Hypergraph-class
Aliases: psimi25Hypergraph-class hyperedgeNodes edgeLabel revInciMat initialize,Hypergraph-method initialize,psimi25Hypergraph-method show,psimi25Hypergraph-method complexes,psimi25Hypergraph-method edgeLabel,psimi25Hypergraph-method hyperedgeNodes,psimi25Hypergraph-method organismName,psimi25Hypergraph-method numEdges,psimi25Hypergraph-method interactorInfo,psimi25Hypergraph-method hyperedgeNodes,Hypergraph-method revInciMat,matrix-method
Keywords: classes
Description: Class "psimi25Hypergraph"
URL: ../../../library/RpsiXML/html/psimi25Hypergraph-class.html

Entry: psimi25Interaction-class
Aliases: psimi25Interaction-class interactionType,psimi25Interaction-method show,psimi25Interaction-method bait,psimi25Interaction-method prey,psimi25Interaction-method confidenceValue,psimi25Interaction-method inhibitor,psimi25Interaction-method neutralComponent,psimi25Interaction-method participant,psimi25Interaction-method pubmedID,psimi25Interaction-method
Keywords: classes
Description: Class "psimi25Interaction"
URL: ../../../library/RpsiXML/html/psimi25Interaction-class.html

Entry: psimi25InteractionEntry-class
Aliases: psimi25InteractionEntry-class interactions,psimi25InteractionEntry-method interactors,psimi25InteractionEntry-method organismName,psimi25InteractionEntry-method releaseDate,psimi25InteractionEntry-method show,psimi25InteractionEntry-method taxId,psimi25InteractionEntry-method
Keywords: classes
Description: Class "psimi25InteractionEntry"
URL: ../../../library/RpsiXML/html/psimi25InteractionEntry-class.html

Entry: psimi25Interactor-class
Aliases: psimi25Interactor-class show,psimi25Interactor-method xref,psimi25Interactor-method
Keywords: classes
Description: A class representing interactor from PSI-MI 2.5 XML files
URL: ../../../library/RpsiXML/html/psimi25Interactor-class.html

Entry: psimi25Source-class
Aliases: psimi25Source-class parseComplex,psimi25Source-method parseExperiment,psimi25Source-method parseInteractor,psimi25Source-method uniprot,psimi25Source-method
Keywords: classes
Description: Class "psimi25Source"
URL: ../../../library/RpsiXML/html/psimi25Source-class.html

Entry: psimi25XML2Graph
Aliases: psimi25XML2Graph interactionEntry2graph complexEntry2graph
Keywords: models
Description: Convert a vector of PSI-MI 2.5 XML files into graph objects
URL: ../../../library/RpsiXML/html/psimi25XML2Graph.html

Entry: releaseDate
Aliases: releaseDate
Keywords: models
Description: Release date of the psimi25InteractionEntry object
URL: ../../../library/RpsiXML/html/releaseDate.html

Entry: separateXMLDataByExpt
Aliases: separateXMLDataByExpt
Keywords: models
Description: Convert a vector of PSI-MI 2.5 XML files into graph objects based on pubmedID
URL: ../../../library/RpsiXML/html/separateXMLDataByExpt.html

Entry: sourceDb-methods
Aliases: sourceDb-methods sourceDb,psimi25Complex-method sourceDb,psimi25Interaction-method sourceDb,psimi25Interactor-method sourceDb,psimi25Source-method
Keywords: methods models
Description: Get source database name
URL: ../../../library/RpsiXML/html/sourceDb-methods.html

Entry: sourceDb
Aliases: sourceDb
Keywords: models
Description: Extracts the source database of the given parameter
URL: ../../../library/RpsiXML/html/sourceDb.html

Entry: sourceId-methods
Aliases: sourceId-methods sourceId,psimi25Complex-method sourceId,psimi25Interaction-method sourceId,psimi25Interactor-method
Keywords: methods models
Description: Extracting ID in the source database
URL: ../../../library/RpsiXML/html/sourceId-methods.html

Entry: sourceId
Aliases: sourceId
Keywords: models
Description: Extracts the source database ID of the given paramter
URL: ../../../library/RpsiXML/html/sourceId.html

Entry: taxId-methods
Aliases: taxId-methods taxId,psimi25Complex-method taxId,psimi25Interactor-method
Keywords: methods
Description: Methods for function taxId
URL: ../../../library/RpsiXML/html/taxId-methods.html

Entry: taxId
Aliases: taxId
Keywords: models
Description: The taxonomy ID of the given parameter
URL: ../../../library/RpsiXML/html/taxId.html

Entry: translateID-methods
Aliases: translateID-methods translateID,psimi25Graph-method translateID,psimi25Hypergraph-method translateID,psimi25Interactor-method translateID,list-method
Keywords: methods models
Description: Translate interactors into other identifiers
URL: ../../../library/RpsiXML/html/translateID-methods.html

Entry: translateID
Aliases: translateID
Keywords: models
Description: Finds identifiers of a given object
URL: ../../../library/RpsiXML/html/translateID.html

Entry: uniprot-methods
Aliases: uniprot-methods uniprot,psimi25Interactor-method
Keywords: methods
Description: Methods for Function uniprot in Package 'RpsiXML'
URL: ../../../library/RpsiXML/html/uniprot-methods.html

Entry: uniprot
Aliases: uniprot
Keywords: models
Description: The UniProt Identifier in the PSI-MI 2.5 XML file
URL: ../../../library/RpsiXML/html/uniprot.html

Entry: validatePSIMI25
Aliases: validatePSIMI25
Keywords: models
Description: Validating PSI-MI 2.5 file with MIF25 XML schema
URL: ../../../library/RpsiXML/html/validatePSIMI25.html
