RpsiXML: R interface to PSI-MI 2.5 files

Queries, data structure and interface to visualization of interaction datasets. This package inplements the PSI-MI 2.5 standard and supports up to now 8 databases. Further databases supporting PSI-MI 2.5 standard will be added continuously.

AuthorJitao David Zhang, Stefan Wiemann, Marc Carlson, with contributions from Tony Chiang
Date of publicationNone
MaintainerJitao David Zhang <jitao_david.zhang@roche.com>
LicenseLGPL-3
Version2.16.0
http://www.bioconductor.org

View on Bioconductor

Man pages

availableXrefs: Get cross reference(s) of interactors from PSI-MI 2.5 files

availableXrefs-methods: Methods for function availableXrefs

bait: Extract bait, prey, participant, inhibitor, pubmed,...

BIOGRID.PSIMI25: Supported PSI-MI 2.5 XML data sources

buildPCHypergraph: Build protein complex hypergraph from PSI-MI 2.5 files

complexes: Extract complexes from psimi25ComplexEntry

complexName: Accessor functions for complex

eListHandler: xmlEventParse handlers for PSI-MI XML documents

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

graphSpeciesConverter: maps one type of grap onto another

interactions: List interactions in the given psimi25InteractionEntry object

interactionType: Type of the interaction

interactorInfo: Interactor info in a matrix

interactorInfo-methods: Methods for Function interactorInfo in Package 'RpsiXML'

interactors: Get information of interactors of the given object

list2Matrix: Converts list into matrix

null2na: Turns null or NA into character "NA"

numInteractions-methods: Get interaction number of the given object

parsePsimi25Interaction: Parsing PSI-MI 2.5 XML documents into interactions

psimi25Attribute-class: Class "psimi25Attribute"

psimi25Complex-class: Class "psimi25Complex"

psimi25ComplexEntry-class: Class "psimi25ComplexEntry"

psimi25Experiment-class: Class "psimi25Experiment"

psimi25Graph-class: Class "psimi25Graph" ~~~

psimi25Hypergraph2GraphNEL: Convert psimi25Hypergraph to graphNEL

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

separateXMLDataByExpt: Convert a vector of PSI-MI 2.5 XML files into graph objects...

sourceId-methods: Extract or set source database name or ID in the source...

taxId-methods: Get or Set the NCBI Taxonomy ID or Organism Name

translateID: Finds identifiers of a given object

translateID-methods: Translate interactors into other identifiers

uniprot: The UniProt Identifier in the PSI-MI 2.5 XML file

uniprot-methods: Methods for Function uniprot in Package 'RpsiXML'

validatePSIMI25: Validating PSI-MI 2.5 file with MIF25 XML schema

Functions

abstract,psimi25GraphBase-method Man page
attributesList Man page
attributesList,attributesListBase-method Man page
availableXrefs Man page
availableXrefs,list-method Man page
availableXrefs-methods Man page
availableXrefs,psimi25InteractionEntry-method Man page
availableXrefs,psimi25Interactor-method Man page
bait Man page
bait,psimi25Interaction-method Man page
BIOGRID.PSIMI25 Man page
buildPCHypergraph Man page
complexEntry2graph Man page
complexes Man page
complexes,psimi25ComplexEntry-method Man page
complexes,psimi25Hypergraph-method Man page
complexName Man page
complexName,psimi25Complex-method Man page
confidenceValue Man page
confidenceValue,psimi25Interaction-method Man page
CORUM.PSIMI25 Man page
DIP.PSIMI25 Man page
edgeLabel Man page
edgeLabel,psimi25Hypergraph-method Man page
eListHandler Man page
getAbstractByPMID Man page
graphConverter Man page
HPRD.PSIMI25 Man page
hyperedgeNodes Man page
hyperedgeNodes,Hypergraph-method Man page
hyperedgeNodes,psimi25Hypergraph-method Man page
hyperGraphConverter Man page
iListHandler Man page
inhibitor Man page
inhibitor,psimi25Interaction-method Man page
initialize,Hypergraph-method Man page
initialize,psimi25Hypergraph-method Man page
INTACT.PSIMI25 Man page
interactionEntry2graph Man page
interactions Man page
interactions,psimi25InteractionEntry-method Man page
interactionType Man page
interactionType,psimi25InteractionElementType-method Man page
interactionType,psimi25Interaction-method Man page
interactorInfo Man page
interactorInfo,list-method Man page
interactorInfo-methods Man page
interactorInfo,psimi25ComplexEntry-method Man page
interactorInfo,psimi25Graph-method Man page
interactorInfo,psimi25Hypergraph-method Man page
interactorInfo,psimi25InteractionEntry-method Man page
interactors Man page
interactors<- Man page
interactors<-,interactorListBase,list-method Man page
interactors,interactorListBase-method Man page
interactors<-,interactorListBase,NULL-method Man page
interactors<--methods Man page
interactors-methods Man page
interactors,psimi25ComplexEntry-method Man page
interactors,psimi25InteractionEntry-method Man page
iValue<-,psimi25Attribute-method Man page
iValue,psimi25Attribute-method Man page
list2Matrix Man page
MATRIXDB.PSIMI25 Man page
members Man page
members,psimi25Complex-method Man page
MINT.PSIMI25 Man page
MIPS.PSIMI25 Man page
MPACT.PSIMI25 Man page
nameAc<-,psimi25Attribute-method Man page
nameAc,psimi25Attribute-method Man page
name<-,psimi25Attribute,ANY-method Man page
name<-,psimi25Attribute,character-method Man page
name,psimi25Attribute-method Man page
neutralComponent Man page
neutralComponent,psimi25Interaction-method Man page
null2na Man page
numEdges,psimi25Hypergraph-method Man page
numInteractions Man page
numInteractions-methods Man page
numInteractions,psimi25InteractionEntry-method Man page
numInteractors Man page
numInteractors,interactorListBase-method Man page
numInteractors-methods Man page
organismName Man page
organismName<- Man page
organismName-methods Man page
organismName<-,organismTaxIdAndName,character-method Man page
organismName,organismTaxIdAndName-method Man page
organismName,psimi25Hypergraph-method Man page
organismName,psimi25InteractionEntry-method Man page
parsePsimi25Complex Man page
parsePsimi25Interaction Man page
participant Man page
participant,psimi25Interaction-method Man page
prey Man page
prey,psimi25Interaction-method Man page
psimi25Attribute-class Man page
psimi25Complex-class Man page
psimi25ComplexEntry-class Man page
psimi25Experiment-class Man page
psimi25Graph-class Man page
psimi25Hypergraph2GraphNEL Man page
psimi25Hypergraph-class Man page
psimi25Interaction-class Man page
psimi25InteractionEntry-class Man page
psimi25Interactor-class Man page
psimi25Source-class Man page
psimi25XML2Graph Man page
pubmedID Man page
pubmedID,psimi25InteractionEntry-method Man page
pubmedID,psimi25Interaction-method Man page
releaseDate Man page
releaseDate-methods Man page
releaseDate,psimi25Entry-method Man page
revInciMat Man page
revInciMat,matrix-method Man page
separateXMLDataByExpt Man page
show,pattributesListBase-method Man page
show,psimi25Attribute-method Man page
show,psimi25AvailabilityType-method Man page
show,psimi25ComplexEntry-method Man page
show,psimi25Complex-method Man page
show,psimi25DbReferenceType-method Man page
show,psimi25Graph-method Man page
show,psimi25Hypergraph-method Man page
show,psimi25InteractionEntry-method Man page
show,psimi25Interaction-method Man page
show,psimi25Interactor-method Man page
show,psimi25NamesType-method Man page
sourceDb Man page
sourceDb<- Man page
"sourceDb<-"-methods Man page
sourceDb-methods Man page
sourceDb,psimi25Source-method Man page
sourceDb<-,sourceDbAndId,character-method Man page
sourceDb,sourceDbAndId-method Man page
sourceId Man page
sourceId<- Man page
"sourceId<-"-methods Man page
sourceId-methods Man page
sourceId<-,sourceDbAndId,character-method Man page
sourceId,sourceDbAndId-method Man page
taxId Man page
taxId<- Man page
taxId-methods Man page
taxId<-,organismTaxIdAndName,character-method Man page
taxId,organismTaxIdAndName-method Man page
taxId,psimi25InteractionEntry-method Man page
translateID Man page
translateID,list-method Man page
translateID-methods Man page
translateID,psimi25Graph-method Man page
translateID,psimi25Hypergraph-method Man page
translateID,psimi25Interactor-method Man page
uniprot Man page
uniprot-methods Man page
uniprot,psimi25Interactor-method Man page
uniprot,psimi25Source-method Man page
validatePSIMI25 Man page
value<-,psimi25Attribute-method Man page
xref Man page
xref,psimi25CommonNameRef-method Man page
xref,psimi25Interactor-method Man page

Files

RpsiXML/DESCRIPTION
RpsiXML/Makefile
RpsiXML/NAMESPACE
RpsiXML/NEWS
RpsiXML/R
RpsiXML/R/AllClasses.R RpsiXML/R/AllGenerics.R RpsiXML/R/AllMethods.R RpsiXML/R/SAXhandlers.R RpsiXML/R/funcsAnnotation.R RpsiXML/R/graphSpeciesConverter.R RpsiXML/R/hyperGraphs.R RpsiXML/R/psi25parser.R RpsiXML/R/psimi25Source.R RpsiXML/R/validatePSIMI25.R
RpsiXML/build
RpsiXML/build/vignette.rds
RpsiXML/inst
RpsiXML/inst/TODO
RpsiXML/inst/doc
RpsiXML/inst/doc/RpsiXML.R
RpsiXML/inst/doc/RpsiXML.Rnw
RpsiXML/inst/doc/RpsiXML.pdf
RpsiXML/inst/doc/RpsiXMLApp.R
RpsiXML/inst/doc/RpsiXMLApp.Rnw
RpsiXML/inst/doc/RpsiXMLApp.pdf
RpsiXML/inst/extdata
RpsiXML/inst/extdata/psi25files
RpsiXML/inst/extdata/psi25files/biogrid_200804_test.xml
RpsiXML/inst/extdata/psi25files/dip_2008_test.xml
RpsiXML/inst/extdata/psi25files/hprd_200709_test.xml
RpsiXML/inst/extdata/psi25files/human_stelzl-2005-1_01.xml
RpsiXML/inst/extdata/psi25files/human_stelzl-2005-1_02.xml
RpsiXML/inst/extdata/psi25files/intact_2008_test.xml
RpsiXML/inst/extdata/psi25files/intact_complexSample.xml
RpsiXML/inst/extdata/psi25files/matrixdb_20080609.xml
RpsiXML/inst/extdata/psi25files/mint_200711_test.xml
RpsiXML/inst/extdata/psi25files/mips_2007_test.xml
RpsiXML/inst/extdata/schemas
RpsiXML/inst/extdata/schemas/MIF25.xsd
RpsiXML/man
RpsiXML/man/BIOGRID.PSIMI25.Rd RpsiXML/man/availableXrefs-methods.Rd RpsiXML/man/availableXrefs.Rd RpsiXML/man/bait.Rd RpsiXML/man/buildPCHypergraph.Rd RpsiXML/man/complexName.Rd RpsiXML/man/complexes.Rd RpsiXML/man/eListHandler.Rd RpsiXML/man/getAbstractByPMID.Rd RpsiXML/man/graphSpeciesConverter.Rd RpsiXML/man/interactionType.Rd RpsiXML/man/interactions.Rd RpsiXML/man/interactorInfo-methods.Rd RpsiXML/man/interactorInfo.Rd RpsiXML/man/interactors.Rd RpsiXML/man/list2Matrix.Rd RpsiXML/man/null2na.Rd RpsiXML/man/numInteractions-methods.Rd RpsiXML/man/parsePsimi25Interaction.Rd RpsiXML/man/psimi25Attribute-class.Rd RpsiXML/man/psimi25Complex-class.Rd RpsiXML/man/psimi25ComplexEntry-class.Rd RpsiXML/man/psimi25Experiment-class.Rd RpsiXML/man/psimi25Graph-class.Rd RpsiXML/man/psimi25Hypergraph-class.Rd RpsiXML/man/psimi25Hypergraph2GraphNEL.Rd RpsiXML/man/psimi25Interaction-class.Rd RpsiXML/man/psimi25InteractionEntry-class.Rd RpsiXML/man/psimi25Interactor-class.Rd RpsiXML/man/psimi25Source-class.Rd RpsiXML/man/psimi25XML2Graph.Rd RpsiXML/man/separateXMLDataByExpt.Rd RpsiXML/man/sourceId-methods.Rd RpsiXML/man/taxId-methods.Rd RpsiXML/man/translateID-methods.Rd RpsiXML/man/translateID.Rd RpsiXML/man/uniprot-methods.Rd RpsiXML/man/uniprot.Rd RpsiXML/man/validatePSIMI25.Rd
RpsiXML/tests
RpsiXML/tests/psimi25Source_test.R
RpsiXML/tests/unitTests
RpsiXML/vignettes
RpsiXML/vignettes/RpsiXML.Rnw
RpsiXML/vignettes/RpsiXMLApp.Rnw
RpsiXML/vignettes/underscore.sty

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