RpsiXML: R interface to PSI-MI 2.5 files

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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.

Author
Jitao David Zhang, Stefan Wiemann, Marc Carlson, with contributions from Tony Chiang
Date of publication
None
Maintainer
Jitao David Zhang <jitao_david.zhang@roche.com>
License
LGPL-3
Version
2.16.0
URLs

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

Files in this package

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