RpsiXML v2.8.0

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.

Functions in RpsiXML

Name Description
complexName Accessor functions for complex
availableXrefs-methods Methods for function availableXrefs
BIOGRID.PSIMI25 Supported PSI-MI 2.5 XML data sources
bait Extract bait, prey, participant, inhibitor, pubmed, confidence value, interaction type, or neutral component information from an object of psimi25Interaction-class
eListHandler xmlEventParse handlers for PSI-MI XML documents
graphConverter maps one type of grap onto another
availableXrefs Get cross reference(s) of interactors from PSI-MI 2.5 files
complexes Extract complexes from psimi25ComplexEntry
getAbstractByPMID A function to obtain the abstract information via a Pubmed ID
buildPCHypergraph Build protein complex hypergraph from PSI-MI 2.5 files
interactors Get information of interactors of the given object
list2Matrix Converts list into matrix
null2na Turns null or NA into character "NA"
interactorInfo Interactor info in a matrix
interactions List interactions in the given psimi25InteractionEntry object
interactorInfo-methods Methods for Function interactorInfo in Package `RpsiXML'
numInteractions-methods Get interaction number of the given object
interactionType Type of the interaction
psimi25Attribute-class Class "psimi25Attribute"
parsePsimi25Interaction Parsing PSI-MI 2.5 XML documents into interactions
psimi25Experiment-class Class "psimi25Experiment"
psimi25Graph-class Class "psimi25Graph" ~~~
psimi25Interactor-class A class representing interactor from PSI-MI 2.5 XML files
psimi25Source-class Class "psimi25Source"
psimi25InteractionEntry-class Class "psimi25InteractionEntry"
psimi25Interaction-class Class "psimi25Interaction"
psimi25Complex-class Class "psimi25Complex"
psimi25Hypergraph-class Class "psimi25Hypergraph"
psimi25ComplexEntry-class Class "psimi25ComplexEntry"
psimi25Hypergraph2GraphNEL Convert psimi25Hypergraph to graphNEL
uniprot-methods Methods for Function uniprot in Package `RpsiXML'
uniprot The UniProt Identifier in the PSI-MI 2.5 XML file
validatePSIMI25 Validating PSI-MI 2.5 file with MIF25 XML schema
sourceId-methods Extract or set source database name or ID in the source database
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
separateXMLDataByExpt Convert a vector of PSI-MI 2.5 XML files into graph objects based on pubmedID
psimi25XML2Graph Convert a vector of PSI-MI 2.5 XML files into graph objects
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Date 2011-10-28
Collate AllClasses.R AllGenerics.R AllMethods.R SAXhandlers.R funcsAnnotation.R hyperGraphs.R psi25parser.R psimi25Source.R validatePSIMI25.R graphSpeciesConverter.R
License LGPL-3
URL http://www.bioconductor.org
biocViews Infrastructure, Proteomics

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