| 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 |