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A B C D E G H I L M N O P R S T U V X misc
| abstract-method | Class "psimi25Graph" ~~~ |
| attributesList | Accessor functions for complex |
| attributesList-method | Class "psimi25Complex" |
| availableXrefs | Get cross reference(s) of interactors from PSI-MI 2.5 files |
| availableXrefs-method | Methods for function availableXrefs |
| availableXrefs-methods | Methods for function availableXrefs |
| bait | Extract bait, prey, participant, inhibitor, pubmed, confidence value, interaction type, or neutral component information from an object of psimi25Interaction-class |
| bait-method | Class "psimi25Interaction" |
| BIOGRID.PSIMI25 | Supported PSI-MI 2.5 XML data sources |
| buildPCHypergraph | Build protein complex hypergraph from PSI-MI 2.5 files |
| complexEntry2graph | Convert a vector of PSI-MI 2.5 XML files into graph objects |
| complexes | Extract complexes from psimi25ComplexEntry |
| complexes-method | Class "psimi25ComplexEntry" |
| complexes-method | Class "psimi25Hypergraph" |
| complexName | Accessor functions for complex |
| complexName-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-method | Class "psimi25Interaction" |
| CORUM.PSIMI25 | Supported PSI-MI 2.5 XML data sources |
| DIP.PSIMI25 | Supported PSI-MI 2.5 XML data sources |
| edgeLabel | Class "psimi25Hypergraph" |
| edgeLabel-method | Class "psimi25Hypergraph" |
| eListHandler | xmlEventParse handlers for PSI-MI XML documents |
| getAbstractByPMID | A function to obtain the abstract information via a Pubmed ID |
| graphConverter | maps one type of grap onto another |
| HPRD.PSIMI25 | Supported PSI-MI 2.5 XML data sources |
| hyperedgeNodes | Class "psimi25Hypergraph" |
| hyperedgeNodes-method | Class "psimi25Hypergraph" |
| hyperGraphConverter | maps one type of grap onto another |
| 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-method | Class "psimi25Interaction" |
| initialize-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-method | Class "psimi25InteractionEntry" |
| interactionType | Type of the interaction |
| interactionType-method | Type of the interaction |
| interactionType-method | Class "psimi25Interaction" |
| interactorInfo | Interactor info in a matrix |
| interactorInfo-method | Methods for Function interactorInfo in Package 'RpsiXML' |
| interactorInfo-method | Class "psimi25Hypergraph" |
| interactorInfo-methods | Methods for Function interactorInfo in Package 'RpsiXML' |
| interactors | Get information of interactors of the given object |
| interactors-method | Get information of interactors of the given object |
| interactors-method | Class "psimi25ComplexEntry" |
| interactors-method | Class "psimi25InteractionEntry" |
| interactors-methods | Get information of interactors of the given object |
| interactors<- | Get information of interactors of the given object |
| interactors<--method | Get information of interactors of the given object |
| interactors<--methods | Get information of interactors of the given object |
| iValue-method | Class "psimi25Attribute" |
| iValue<--method | Class "psimi25Attribute" |
| list2Matrix | Converts list into matrix |
| MATRIXDB.PSIMI25 | Supported PSI-MI 2.5 XML data sources |
| members | Accessor functions for complex |
| members-method | Class "psimi25Complex" |
| MINT.PSIMI25 | Supported PSI-MI 2.5 XML data sources |
| MIPS.PSIMI25 | Supported PSI-MI 2.5 XML data sources |
| MPACT.PSIMI25 | Supported PSI-MI 2.5 XML data sources |
| name-method | Class "psimi25Attribute" |
| name<--method | Class "psimi25Attribute" |
| nameAc-method | Class "psimi25Attribute" |
| nameAc<--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-method | Class "psimi25Interaction" |
| null2na | Turns null or NA into character "NA" |
| numEdges-method | Class "psimi25Hypergraph" |
| numInteractions | Get interaction number of the given object |
| numInteractions-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-method | Get information of interactors of the given object |
| numInteractors-methods | Get information of interactors of the given object |
| organismName | Get or Set the NCBI Taxonomy ID or Organism Name |
| organismName-method | Class "psimi25Hypergraph" |
| organismName-method | Class "psimi25InteractionEntry" |
| organismName-method | Get or Set the NCBI Taxonomy ID or Organism Name |
| organismName-methods | Get or Set the NCBI Taxonomy ID or Organism Name |
| organismName<- | Get or Set the NCBI Taxonomy ID or Organism Name |
| organismName<--method | Get or Set the NCBI Taxonomy ID or Organism Name |
| 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-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-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-method | Class "psimi25Interaction" |
| pubmedID-method | Class "psimi25InteractionEntry" |
| releaseDate | Class "psimi25InteractionEntry" |
| releaseDate-method | Class "psimi25InteractionEntry" |
| releaseDate-methods | Class "psimi25InteractionEntry" |
| revInciMat | Class "psimi25Hypergraph" |
| revInciMat-method | Class "psimi25Hypergraph" |
| separateXMLDataByExpt | Convert a vector of PSI-MI 2.5 XML files into graph objects based on pubmedID |
| show-method | Class "psimi25Attribute" |
| show-method | Class "psimi25Complex" |
| show-method | Class "psimi25ComplexEntry" |
| show-method | Class "psimi25Graph" ~~~ |
| show-method | Class "psimi25Hypergraph" |
| show-method | Class "psimi25Interaction" |
| show-method | Class "psimi25InteractionEntry" |
| show-method | A class representing interactor from PSI-MI 2.5 XML files |
| sourceDb | Extract or set source database name or ID in the source database |
| sourceDb-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<--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-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<--method | Extract or set source database name or ID in the source database |
| taxId | Get or Set the NCBI Taxonomy ID or Organism Name |
| taxId-method | Class "psimi25InteractionEntry" |
| taxId-method | Get or Set the NCBI Taxonomy ID or Organism Name |
| taxId-methods | Get or Set the NCBI Taxonomy ID or Organism Name |
| taxId<- | Get or Set the NCBI Taxonomy ID or Organism Name |
| taxId<--method | Get or Set the NCBI Taxonomy ID or Organism Name |
| translateID | Finds identifiers of a given object |
| translateID-method | Translate interactors into other identifiers |
| translateID-methods | Translate interactors into other identifiers |
| uniprot | The UniProt Identifier in the PSI-MI 2.5 XML file |
| uniprot-method | Class "psimi25Source" |
| uniprot-method | Methods for Function uniprot in Package 'RpsiXML' |
| uniprot-methods | Methods for Function uniprot in Package 'RpsiXML' |
| validatePSIMI25 | Validating PSI-MI 2.5 file with MIF25 XML schema |
| value<--method | Class "psimi25Attribute" |
| xref | Get cross reference(s) of interactors from PSI-MI 2.5 files |
| xref-method | Class "psimi25Attribute" |
| xref-method | A class representing interactor from PSI-MI 2.5 XML files |
| "sourceDb<-"-methods | 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 |