RpsiXML: R interface to PSI-MI 2.5 files
Version 2.18.0

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.

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AuthorJitao David Zhang, Stefan Wiemann, Marc Carlson, with contributions from Tony Chiang
Bioconductor views Infrastructure Proteomics
Date of publicationNone
MaintainerJitao David Zhang <jitao_david.zhang@roche.com>
LicenseLGPL-3
Version2.18.0
URL http://www.bioconductor.org
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("RpsiXML")

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

"sourceDb<-"-methods Man page
"sourceId<-"-methods Man page
BIOGRID.PSIMI25 Man page
CORUM.PSIMI25 Man page
DIP.PSIMI25 Man page
HPRD.PSIMI25 Man page
INTACT.PSIMI25 Man page
MATRIXDB.PSIMI25 Man page
MINT.PSIMI25 Man page
MIPS.PSIMI25 Man page
MPACT.PSIMI25 Man page
XMLattributeValueByPath Source code
XMLvalueByPath Source code
abstract,psimi25GraphBase-method Man page
annotateComplexesWithInteractors Source code
attributesList Man page
attributesList,attributesListBase-method Man page
availableXrefs Man page
availableXrefs,list-method Man page
availableXrefs,psimi25InteractionEntry-method Man page
availableXrefs,psimi25Interactor-method Man page
availableXrefs-methods Man page
bait Man page
bait,psimi25Interaction-method Man page
buildPCHypergraph Man page Source code
complexEntry2graph Man page Source code
complexName Man page
complexName,psimi25Complex-method Man page
complexes Man page
complexes,psimi25ComplexEntry-method Man page
complexes,psimi25Hypergraph-method Man page
confidenceValue Man page
confidenceValue,psimi25Interaction-method Man page
eListHandler Man page Source code
edgeLabel Man page
edgeLabel,psimi25Hypergraph-method Man page
genBPGraph Source code Source code
getAbstractByPMID Man page Source code
getDesired Source code
getEntryBasePath Source code
getExperimentNodeSetPath Source code
getHorizontalSepLine Source code
getInteractionNodeSet Source code
getInteractionNodeSetPath Source code
getInteractionPubmedPath Source code
getInteractorNodeSet Source code
getPrimaryInteractorPath Source code
getReleaseDatePath Source code
getSecondaryInteractorPath Source code
getValueByMatchingMatrixColumn Source code
getXmlExperimentNodeSet Source code
graphConverter Man page Source code
hyperGraphConverter Man page Source code
hyperedgeNodes Man page
hyperedgeNodes,Hypergraph-method Man page
hyperedgeNodes,psimi25Hypergraph-method Man page
iListHandler Man page Source code
iValue,psimi25Attribute-method Man page
iValue<-,psimi25Attribute-method Man page
inhibitor Man page
inhibitor,psimi25Interaction-method Man page
initialize,Hypergraph-method Man page
initialize,psimi25Hypergraph-method Man page
interactionEntry2graph Man page Source code
interactionType Man page
interactionType,psimi25Interaction-method Man page
interactionType,psimi25InteractionElementType-method Man page
interactions Man page
interactions,psimi25InteractionEntry-method Man page
interactorInfo Man page
interactorInfo,list-method Man page
interactorInfo,psimi25ComplexEntry-method Man page
interactorInfo,psimi25Graph-method Man page
interactorInfo,psimi25Hypergraph-method Man page
interactorInfo,psimi25InteractionEntry-method Man page
interactorInfo-methods Man page
interactors Man page
interactors,interactorListBase-method Man page
interactors,psimi25ComplexEntry-method Man page
interactors,psimi25InteractionEntry-method Man page
interactors-methods Man page
interactors<- Man page
interactors<-,interactorListBase,NULL-method Man page
interactors<-,interactorListBase,list-method Man page
interactors<--methods Man page
isLengthOneAndNA Source code
list2Matrix Man page Source code
members Man page
members,psimi25Complex-method Man page
name,psimi25Attribute-method Man page
name<-,psimi25Attribute,ANY-method Man page
name<-,psimi25Attribute,character-method Man page
nameAc,psimi25Attribute-method Man page
nameAc<-,psimi25Attribute-method Man page
neutralComponent Man page
neutralComponent,psimi25Interaction-method Man page
nonNullXMLattributeValueByPath Source code
nonNullXMLvalueByPath Source code
null2na Man page Source code
numEdges,psimi25Hypergraph-method Man page
numInteractions Man page
numInteractions,psimi25InteractionEntry-method Man page
numInteractions-methods Man page
numInteractors Man page
numInteractors,interactorListBase-method Man page
numInteractors-methods Man page
organismName Man page
organismName,organismTaxIdAndName-method Man page
organismName,psimi25Hypergraph-method Man page
organismName,psimi25InteractionEntry-method Man page
organismName-methods Man page
organismName<- Man page
organismName<-,organismTaxIdAndName,character-method Man page
parsePsimi25Complex Man page Source code
parsePsimi25Interaction Man page Source code
parseReleaseDate Source code
parseXmlAttribute Source code
parseXmlAttributeNodeSet Source code
parseXmlAttributesListByPath Source code
parseXmlComplexNode Source code
parseXmlEntryInteractors Source code
parseXmlEntryNode Source code
parseXmlEntryNodeSet Source code
parseXmlExperimentNode Source code
parseXmlExperimentNodeSet Source code
parseXmlInteractionNode Source code
parseXmlInteractionNodeSet Source code
parseXmlInteractorNode Source code
parseXmlInteractorNodeSet Source code
participant Man page
participant,psimi25Interaction-method Man page
prey Man page
prey,psimi25Interaction-method Man page
printManyItems Source code
psimi25Attribute-class Man page
psimi25Complex-class Man page
psimi25ComplexEntry-class Man page
psimi25Experiment-class Man page
psimi25Graph-class Man page
psimi25Hypergraph-class Man page
psimi25Hypergraph2GraphNEL Man page Source code
psimi25Interaction-class Man page
psimi25InteractionEntry-class Man page
psimi25Interactor-class Man page
psimi25Source-class Man page
psimi25XML2Graph Man page Source code
pubmedID Man page
pubmedID,psimi25Interaction-method Man page
pubmedID,psimi25InteractionEntry-method Man page
quiteAsInteger Source code
releaseDate Man page
releaseDate,psimi25Entry-method Man page
releaseDate-methods Man page
removeHypergraphNAnode Source code
revInciMat Man page
revInciMat,matrix-method Man page
separateXMLDataByExpt Man page Source code
show,pattributesListBase-method Man page
show,psimi25Attribute-method Man page
show,psimi25AvailabilityType-method Man page
show,psimi25Complex-method Man page
show,psimi25ComplexEntry-method Man page
show,psimi25DbReferenceType-method Man page
show,psimi25Graph-method Man page
show,psimi25Hypergraph-method Man page
show,psimi25Interaction-method Man page
show,psimi25InteractionEntry-method Man page
show,psimi25Interactor-method Man page
show,psimi25NamesType-method Man page
showHorizontalSepLine Source code
showListWithoutNames Source code
sourceDb Man page
sourceDb,psimi25Source-method Man page
sourceDb,sourceDbAndId-method Man page
sourceDb-methods Man page
sourceDb<- Man page
sourceDb<-,sourceDbAndId,character-method Man page
sourceId Man page
sourceId,sourceDbAndId-method Man page
sourceId-methods Man page
sourceId<- Man page
sourceId<-,sourceDbAndId,character-method Man page
statusDisplay Source code
statusIndicator Source code
taxId Man page
taxId,organismTaxIdAndName-method Man page
taxId,psimi25InteractionEntry-method Man page
taxId-methods Man page
taxId<- Man page
taxId<-,organismTaxIdAndName,character-method Man page
translateID Man page
translateID,list-method Man page
translateID,psimi25Graph-method Man page
translateID,psimi25Hypergraph-method Man page
translateID,psimi25Interactor-method Man page
translateID-methods Man page
uniprot Man page
uniprot,psimi25Interactor-method Man page
uniprot,psimi25Source-method Man page
uniprot-methods Man page
validatePSIMI25 Man page Source code
value<-,psimi25Attribute-method Man page
xref Man page
xref,psimi25CommonNameRef-method Man page
xref,psimi25Interactor-method Man page

Files

DESCRIPTION
Makefile
NAMESPACE
NEWS
R
R/AllClasses.R
R/AllGenerics.R
R/AllMethods.R
R/SAXhandlers.R
R/funcsAnnotation.R
R/graphSpeciesConverter.R
R/hyperGraphs.R
R/psi25parser.R
R/psimi25Source.R
R/validatePSIMI25.R
build
build/vignette.rds
inst
inst/TODO
inst/doc
inst/doc/RpsiXML.R
inst/doc/RpsiXML.Rnw
inst/doc/RpsiXML.pdf
inst/doc/RpsiXMLApp.R
inst/doc/RpsiXMLApp.Rnw
inst/doc/RpsiXMLApp.pdf
inst/extdata
inst/extdata/psi25files
inst/extdata/psi25files/biogrid_200804_test.xml
inst/extdata/psi25files/dip_2008_test.xml
inst/extdata/psi25files/hprd_200709_test.xml
inst/extdata/psi25files/human_stelzl-2005-1_01.xml
inst/extdata/psi25files/human_stelzl-2005-1_02.xml
inst/extdata/psi25files/intact_2008_test.xml
inst/extdata/psi25files/intact_complexSample.xml
inst/extdata/psi25files/matrixdb_20080609.xml
inst/extdata/psi25files/mint_200711_test.xml
inst/extdata/psi25files/mips_2007_test.xml
inst/extdata/schemas
inst/extdata/schemas/MIF25.xsd
man
man/BIOGRID.PSIMI25.Rd
man/availableXrefs-methods.Rd
man/availableXrefs.Rd
man/bait.Rd
man/buildPCHypergraph.Rd
man/complexName.Rd
man/complexes.Rd
man/eListHandler.Rd
man/getAbstractByPMID.Rd
man/graphSpeciesConverter.Rd
man/interactionType.Rd
man/interactions.Rd
man/interactorInfo-methods.Rd
man/interactorInfo.Rd
man/interactors.Rd
man/list2Matrix.Rd
man/null2na.Rd
man/numInteractions-methods.Rd
man/parsePsimi25Interaction.Rd
man/psimi25Attribute-class.Rd
man/psimi25Complex-class.Rd
man/psimi25ComplexEntry-class.Rd
man/psimi25Experiment-class.Rd
man/psimi25Graph-class.Rd
man/psimi25Hypergraph-class.Rd
man/psimi25Hypergraph2GraphNEL.Rd
man/psimi25Interaction-class.Rd
man/psimi25InteractionEntry-class.Rd
man/psimi25Interactor-class.Rd
man/psimi25Source-class.Rd
man/psimi25XML2Graph.Rd
man/separateXMLDataByExpt.Rd
man/sourceId-methods.Rd
man/taxId-methods.Rd
man/translateID-methods.Rd
man/translateID.Rd
man/uniprot-methods.Rd
man/uniprot.Rd
man/validatePSIMI25.Rd
tests
tests/psimi25Source_test.R
tests/unitTests
vignettes
vignettes/RpsiXML.Rnw
vignettes/RpsiXMLApp.Rnw
vignettes/underscore.sty
RpsiXML documentation built on May 20, 2017, 9:22 p.m.