complexEntry2graph |
Convert a vector of PSI-MI 2.5 XML files into graph objects |
complexes |
Extract complexes from psimi25ComplexEntry |
complexes,psimi25ComplexEntry-method |
Class "psimi25ComplexEntry" |
complexes,psimi25Hypergraph-method |
Class "psimi25Hypergraph" |
complexName |
Accessor functions for complex |
complexName,psimi25Complex-method |
Class "psimi25Complex" |
confidenceValue |
Extract bait, prey, participant, inhibitor, pubmed, confidence value, interaction type,
or neutral component information from an object of psimi25Interaction-class |
confidenceValue,psimi25Interaction-method |
Class "psimi25Interaction" |
CORUM.PSIMI25 |
Supported PSI-MI 2.5 XML data sources |
iListHandler |
xmlEventParse handlers for PSI-MI XML documents |
inhibitor |
Extract bait, prey, participant, inhibitor, pubmed, confidence value, interaction type,
or neutral component information from an object of psimi25Interaction-class |
inhibitor,psimi25Interaction-method |
Class "psimi25Interaction" |
initialize,Hypergraph-method |
Class "psimi25Hypergraph" |
initialize,psimi25Hypergraph-method |
Class "psimi25Hypergraph" |
INTACT.PSIMI25 |
Supported PSI-MI 2.5 XML data sources |
interactionEntry2graph |
Convert a vector of PSI-MI 2.5 XML files into graph objects |
interactions |
List interactions in the given psimi25InteractionEntry object |
interactions,psimi25InteractionEntry-method |
Class "psimi25InteractionEntry" |
interactionType |
Type of the interaction |
interactionType,psimi25Interaction-method |
Class "psimi25Interaction" |
interactionType,psimi25InteractionElementType-method |
Type of the interaction |
interactorInfo |
Interactor info in a matrix |
interactorInfo,list-method |
Methods for Function interactorInfo in Package 'RpsiXML' |
interactorInfo,psimi25ComplexEntry-method |
Methods for Function interactorInfo in Package 'RpsiXML' |
interactorInfo,psimi25Graph-method |
Methods for Function interactorInfo in Package 'RpsiXML' |
interactorInfo,psimi25Hypergraph-method |
Class "psimi25Hypergraph" |
interactorInfo,psimi25InteractionEntry-method |
Methods for Function interactorInfo in Package 'RpsiXML' |
interactorInfo-methods |
Methods for Function interactorInfo in Package 'RpsiXML' |
interactors |
Get information of interactors of the given object |
interactors,interactorListBase-method |
Get information of interactors of the given object |
interactors,psimi25ComplexEntry-method |
Class "psimi25ComplexEntry" |
interactors,psimi25InteractionEntry-method |
Class "psimi25InteractionEntry" |
interactors-methods |
Get information of interactors of the given object |
interactors<- |
Get information of interactors of the given object |
interactors<-,interactorListBase,list-method |
Get information of interactors of the given object |
interactors<-,interactorListBase,NULL-method |
Get information of interactors of the given object |
interactors<--methods |
Get information of interactors of the given object |
iValue,psimi25Attribute-method |
Class "psimi25Attribute" |
iValue<-,psimi25Attribute-method |
Class "psimi25Attribute" |
name,psimi25Attribute-method |
Class "psimi25Attribute" |
name<-,psimi25Attribute,ANY-method |
Class "psimi25Attribute" |
name<-,psimi25Attribute,character-method |
Class "psimi25Attribute" |
nameAc,psimi25Attribute-method |
Class "psimi25Attribute" |
nameAc<-,psimi25Attribute-method |
Class "psimi25Attribute" |
neutralComponent |
Extract bait, prey, participant, inhibitor, pubmed, confidence value, interaction type,
or neutral component information from an object of psimi25Interaction-class |
neutralComponent,psimi25Interaction-method |
Class "psimi25Interaction" |
null2na |
Turns null or NA into character "NA" |
numEdges,psimi25Hypergraph-method |
Class "psimi25Hypergraph" |
numInteractions |
Get interaction number of the given object |
numInteractions,psimi25InteractionEntry-method |
Get interaction number of the given object |
numInteractions-methods |
Get interaction number of the given object |
numInteractors |
Get information of interactors of the given object |
numInteractors,interactorListBase-method |
Get information of interactors of the given object |
numInteractors-methods |
Get information of interactors of the given object |
parsePsimi25Complex |
Parsing PSI-MI 2.5 XML documents into interactions |
parsePsimi25Interaction |
Parsing PSI-MI 2.5 XML documents into interactions |
participant |
Extract bait, prey, participant, inhibitor, pubmed, confidence value, interaction type,
or neutral component information from an object of psimi25Interaction-class |
participant,psimi25Interaction-method |
Class "psimi25Interaction" |
prey |
Extract bait, prey, participant, inhibitor, pubmed, confidence value, interaction type,
or neutral component information from an object of psimi25Interaction-class |
prey,psimi25Interaction-method |
Class "psimi25Interaction" |
psimi25Attribute-class |
Class "psimi25Attribute" |
psimi25Complex-class |
Class "psimi25Complex" |
psimi25ComplexEntry-class |
Class "psimi25ComplexEntry" |
psimi25Experiment-class |
Class "psimi25Experiment" |
psimi25Graph-class |
Class "psimi25Graph" ~~~ |
psimi25Hypergraph-class |
Class "psimi25Hypergraph" |
psimi25Hypergraph2GraphNEL |
Convert psimi25Hypergraph to graphNEL |
psimi25Interaction-class |
Class "psimi25Interaction" |
psimi25InteractionEntry-class |
Class "psimi25InteractionEntry" |
psimi25Interactor-class |
A class representing interactor from PSI-MI 2.5 XML files |
psimi25Source-class |
Class "psimi25Source" |
psimi25XML2Graph |
Convert a vector of PSI-MI 2.5 XML files into graph objects |
pubmedID |
Extract bait, prey, participant, inhibitor, pubmed, confidence value, interaction type,
or neutral component information from an object of psimi25Interaction-class |
pubmedID,psimi25Interaction-method |
Class "psimi25Interaction" |
pubmedID,psimi25InteractionEntry-method |
Class "psimi25InteractionEntry" |
separateXMLDataByExpt |
Convert a vector of PSI-MI 2.5 XML files into graph objects based on pubmedID |
show,pattributesListBase-method |
Class "psimi25Complex" |
show,psimi25Attribute-method |
Class "psimi25Attribute" |
show,psimi25AvailabilityType-method |
Class "psimi25Attribute" |
show,psimi25Complex-method |
Class "psimi25Complex" |
show,psimi25ComplexEntry-method |
Class "psimi25ComplexEntry" |
show,psimi25DbReferenceType-method |
Class "psimi25Attribute" |
show,psimi25Graph-method |
Class "psimi25Graph" ~~~ |
show,psimi25Hypergraph-method |
Class "psimi25Hypergraph" |
show,psimi25Interaction-method |
Class "psimi25Interaction" |
show,psimi25InteractionEntry-method |
Class "psimi25InteractionEntry" |
show,psimi25Interactor-method |
A class representing interactor from PSI-MI 2.5 XML files |
show,psimi25NamesType-method |
Class "psimi25Attribute" |
sourceDb |
Extract or set source database name or ID in the source database |
sourceDb,psimi25Source-method |
Extract or set source database name or ID in the source database |
sourceDb,sourceDbAndId-method |
Extract or set source database name or ID in the source database |
sourceDb-methods |
Extract or set source database name or ID in the source database |
sourceDb<- |
Extract or set source database name or ID in the source database |
sourceDb<-,sourceDbAndId,character-method |
Extract or set source database name or ID in the source database |
sourceId |
Extract or set source database name or ID in the source database |
sourceId,sourceDbAndId-method |
Extract or set source database name or ID in the source database |
sourceId-methods |
Extract or set source database name or ID in the source database |
sourceId<- |
Extract or set source database name or ID in the source database |
sourceId<-,sourceDbAndId,character-method |
Extract or set source database name or ID in the source database |