# R interface to PSI-MI 2.5 files

## Documentation for package ‘RpsiXML’ version 1.6.0

## User Guides and Package Vignettes

Read overview or browse directory.

## Help Pages

A B C D E G H I L M N O P R S T U V X

## -- --

"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

## -- A --

abstract,psimi25GraphBase-method | Class "psimi25Graph" ~~~
attributesList | Accessor functions for complex
attributesList,attributesListBase-method | Class "psimi25Complex"
availableXrefs | Get cross reference(s) of interactors from PSI-MI 2.5 files
availableXrefs,list-method | Methods for function availableXrefs
availableXrefs,psimi25InteractionEntry-method | Methods for function availableXrefs
availableXrefs,psimi25Interactor-method | Methods for function availableXrefs
availableXrefs-methods | Methods for function availableXrefs

## -- B --

bait | Extract bait, prey, participant, inhibitor, pubmed, confidence value, interaction type, or neutral component information from an object of psimi25Interaction-class
bait,psimi25Interaction-method | Class "psimi25Interaction"
BIOGRID.PSIMI25 | Supported PSI-MI 2.5 XML data sources
buildPCHypergraph | Build protein complex hypergraph from PSI-MI 2.5 files

## -- C --

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

## -- D --

DIP.PSIMI25 | Supported PSI-MI 2.5 XML data sources

## -- E --

edgeLabel | Class "psimi25Hypergraph"
edgeLabel,psimi25Hypergraph-method | Class "psimi25Hypergraph"
eListHandler | xmlEventParse handlers for PSI-MI XML documents

## -- G --

getAbstractByPMID | A function to obtain the abstract information via a Pubmed ID
graphConverter | maps one type of grap onto another

## -- H --

HPRD.PSIMI25 | Supported PSI-MI 2.5 XML data sources
hyperedgeNodes | Class "psimi25Hypergraph"
hyperedgeNodes,Hypergraph-method | Class "psimi25Hypergraph"
hyperedgeNodes,psimi25Hypergraph-method | Class "psimi25Hypergraph"
hyperGraphConverter | maps one type of grap onto another

## -- I --

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"

## -- L --

list2Matrix | Converts list into matrix

## -- M --

MATRIXDB.PSIMI25 | Supported PSI-MI 2.5 XML data sources
members | Accessor functions for complex
members,psimi25Complex-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

## -- N --

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

## -- O --

organismName | Get or Set the NCBI Taxonomy ID or Organism Name
organismName,organismTaxIdAndName-method | Get or Set the NCBI Taxonomy ID or Organism Name
organismName,psimi25Hypergraph-method | Class "psimi25Hypergraph"
organismName,psimi25InteractionEntry-method | Class "psimi25InteractionEntry"
organismName-methods | Get or Set the NCBI Taxonomy ID or Organism Name
organismName<- | Get or Set the NCBI Taxonomy ID or Organism Name
organismName<-,organismTaxIdAndName,character-method | Get or Set the NCBI Taxonomy ID or Organism Name

## -- P --

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"

## -- R --

releaseDate | Class "psimi25InteractionEntry"
releaseDate,psimi25Entry-method | Class "psimi25InteractionEntry"
releaseDate-methods | Class "psimi25InteractionEntry"
revInciMat | Class "psimi25Hypergraph"
revInciMat,matrix-method | Class "psimi25Hypergraph"

## -- S --

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

## -- T --

taxId | Get or Set the NCBI Taxonomy ID or Organism Name
taxId,organismTaxIdAndName-method | Get or Set the NCBI Taxonomy ID or Organism Name
taxId,psimi25InteractionEntry-method | Class "psimi25InteractionEntry"
taxId-methods | Get or Set the NCBI Taxonomy ID or Organism Name
taxId<- | Get or Set the NCBI Taxonomy ID or Organism Name
taxId<-,organismTaxIdAndName,character-method | Get or Set the NCBI Taxonomy ID or Organism Name
translateID | Finds identifiers of a given object
translateID,list-method | Translate interactors into other identifiers
translateID,psimi25Graph-method | Translate interactors into other identifiers
translateID,psimi25Hypergraph-method | Translate interactors into other identifiers
translateID,psimi25Interactor-method | Translate interactors into other identifiers
translateID-methods | Translate interactors into other identifiers

## -- U --

uniprot | The UniProt Identifier in the PSI-MI 2.5 XML file
uniprot,psimi25Interactor-method | Methods for Function uniprot in Package 'RpsiXML'
uniprot,psimi25Source-method | Class "psimi25Source"
uniprot-methods | Methods for Function uniprot in Package 'RpsiXML'

## -- V --

validatePSIMI25 | Validating PSI-MI 2.5 file with MIF25 XML schema
value<-,psimi25Attribute-method | Class "psimi25Attribute"

## -- X --

xref | Get cross reference(s) of interactors from PSI-MI 2.5 files
xref,psimi25CommonNameRef-method | Class "psimi25Attribute"
xref,psimi25Interactor-method | A class representing interactor from PSI-MI 2.5 XML files