RpsiXML v2.14.0

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
buildPCHypergraph Build protein complex hypergraph from PSI-MI 2.5 files
null2na Turns null or NA into character "NA"
bait Extract bait, prey, participant, inhibitor, pubmed, confidence value, interaction type, or neutral component information from an object of psimi25Interaction-class
psimi25InteractionEntry-class Class "psimi25InteractionEntry"
availableXrefs Get cross reference(s) of interactors from PSI-MI 2.5 files
psimi25Experiment-class Class "psimi25Experiment"
psimi25Interactor-class A class representing interactor from PSI-MI 2.5 XML files
numInteractions-methods Get interaction number of the given object
list2Matrix Converts list into matrix
psimi25Graph-class Class "psimi25Graph" ~~~
psimi25ComplexEntry-class Class "psimi25ComplexEntry"
psimi25Hypergraph-class Class "psimi25Hypergraph"
interactors Get information of interactors of the given object
psimi25XML2Graph 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 database
complexes Extract complexes from psimi25ComplexEntry
complexName Accessor functions for complex
interactionType Type of the interaction
graphConverter maps one type of grap onto another
uniprot The UniProt Identifier in the PSI-MI 2.5 XML file
psimi25Interaction-class Class "psimi25Interaction"
interactorInfo-methods Methods for Function interactorInfo in Package `RpsiXML'
psimi25Hypergraph2GraphNEL Convert psimi25Hypergraph to graphNEL
translateID Finds identifiers of a given object
psimi25Complex-class Class "psimi25Complex"
validatePSIMI25 Validating PSI-MI 2.5 file with MIF25 XML schema
getAbstractByPMID A function to obtain the abstract information via a Pubmed ID
translateID-methods Translate interactors into other identifiers
separateXMLDataByExpt Convert a vector of PSI-MI 2.5 XML files into graph objects based on pubmedID
psimi25Attribute-class Class "psimi25Attribute"
BIOGRID.PSIMI25 Supported PSI-MI 2.5 XML data sources
uniprot-methods Methods for Function uniprot in Package `RpsiXML'
availableXrefs-methods Methods for function availableXrefs
interactions List interactions in the given psimi25InteractionEntry object
parsePsimi25Interaction Parsing PSI-MI 2.5 XML documents into interactions
interactorInfo Interactor info in a matrix
eListHandler xmlEventParse handlers for PSI-MI XML documents
psimi25Source-class Class "psimi25Source"
taxId-methods Get or Set the NCBI Taxonomy ID or Organism Name
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Details

Date 2015-04-09
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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