R interface to PSI-MI 2.5 files


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Documentation for package ‘RpsiXML’ version 1.4.1

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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