R interface to PSI-MI 2.5 files


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Documentation for package ‘RpsiXML’ version 1.0.0

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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

-- C --

complexAttributes Accessor functions for complex
complexes Extract complexes from psimi25ComplexEntry
complexes,psimi25ComplexEntry-method Class "psimi25ComplexEntry"
complexMembers Accessor functions for complex
complexName Accessor functions for complex
confidenceValue Extract bait, prey, participant, inhibitor, pubmed, confidence value, interaction type, or neutral component information from an object of psimi25Interaction-class
CORUM.PSIMI25 Supported PSI-MI 2.5 XML data sources

-- D --

DIP.PSIMI25 Supported PSI-MI 2.5 XML data sources

-- E --

eListHandler xmlEventParse handlers for PSI-MI XML documents

-- G --

getAbstractByPMID A function to obtain the abstract information via a Pubmed ID

-- H --

HPRD.PSIMI25 Supported PSI-MI 2.5 XML data sources

-- 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
initialize,psimi25Hypergraph-method Class "psimi25Hypergraph"
INTACT.PSIMI25 Supported PSI-MI 2.5 XML data sources
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 Methods for Function interactorInfo in Package ‘RpsiXML’
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
null2na Turns null or NA into character "NA"

-- O --

organismName Organism name of the psimi25InteractionEntry
organismName,psimi25InteractionEntry-method Class "psimi25InteractionEntry"

-- 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
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

-- R --

releaseDate Release date of the psimi25InteractionEntry object
releaseDate,psimi25InteractionEntry-method Class "psimi25InteractionEntry"

-- 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-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