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 |