# R interface to PSI-MI 2.5 files

## Documentation for package ‘RpsiXML’ version 1.4.1

## User Guides and Package Vignettes

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## Help Pages

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

## -- A --

abstract,psimi25Graph-method | Class "psimi25Graph" ~~~
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 --

complexAttributes | Accessor functions for complex
complexAttributes,psimi25Complex-method | Class "psimi25Complex"
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"
complexMembers | Accessor functions for complex
complexMembers,psimi25Complex-method | Class "psimi25Complex"
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"
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 | Interactors of the given object
interactors,psimi25ComplexEntry-method | Class "psimi25ComplexEntry"
interactors,psimi25Graph-method | Methods for Function interactors
interactors,psimi25Hypergraph-method | Methods for Function interactors
interactors,psimi25InteractionEntry-method | Class "psimi25InteractionEntry"
interactors-methods | Methods for Function interactors

## -- L --

list2Matrix | Converts list into matrix

## -- M --

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

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 interactor number of the given item
numInteractors,psimi25Hypergraph-method | Get interactor number of the given item
numInteractors,psimi25InteractionEntry-method | Get interactor number of the given item
numInteractors-methods | Get interactor number of the given item

## -- O --

organismName | Returns the organism name(s) of the given item
organismName,psimi25Complex-method | Returns the organism name(s) of the given item
organismName,psimi25Hypergraph-method | Class "psimi25Hypergraph"
organismName,psimi25InteractionEntry-method | Class "psimi25InteractionEntry"
organismName,psimi25Interactor-method | Returns the organism name(s) of the given item
organismName-methods | Returns the organism name(s) of the given item

## -- P --

parseComplex | Parse complex, interactor and experiment from PSI-MI 2.5 XML node
parseComplex,psimi25Source-method | Class "psimi25Source"
parseExperiment | Parse complex, interactor and experiment from PSI-MI 2.5 XML node
parseExperiment,psimi25Source-method | Class "psimi25Source"
parseInteractor | Parse complex, interactor and experiment from PSI-MI 2.5 XML node
parseInteractor,psimi25Source-method | Class "psimi25Source"
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"
psimi25Complex-class | Class "psimi25Complex"
psimi25ComplexEntry-class | Class "psimi25ComplexEntry"
psimi25Experiment-class | Class "psimi25Experiment"
psimi25Graph-class | Class "psimi25Graph" ~~~
psimi25Hypergraph-class | Class "psimi25Hypergraph"
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"

## -- R --

releaseDate | Release date of the psimi25InteractionEntry object
releaseDate,psimi25InteractionEntry-method | 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,psimi25Complex-method | Class "psimi25Complex"
show,psimi25ComplexEntry-method | Class "psimi25ComplexEntry"
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
sourceDb | Extracts the source database of the given parameter
sourceDb,psimi25Complex-method | Get source database name
sourceDb,psimi25Interaction-method | Get source database name
sourceDb,psimi25Interactor-method | Get source database name
sourceDb,psimi25Source-method | Get source database name
sourceDb-methods | Get source database name
sourceId | Extracts the source database ID of the given paramter
sourceId,psimi25Complex-method | Extracting ID in the source database
sourceId,psimi25Interaction-method | Extracting ID in the source database
sourceId,psimi25Interactor-method | Extracting ID in the source database
sourceId-methods | Extracting ID in the source database

## -- T --

taxId | The taxonomy ID of the given parameter
taxId,psimi25Complex-method | Methods for function taxId
taxId,psimi25InteractionEntry-method | Class "psimi25InteractionEntry"
taxId,psimi25Interactor-method | Methods for function taxId
taxId-methods | Methods for function taxId
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

## -- X --

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