R interface to PSI-MI 2.5 files


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Documentation for package ‘RpsiXML’ version 1.6.0

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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