Man pages for alyst/RpsiXML
R interface to PSI-MI 2.5 files

availableXrefsGet cross reference(s) of interactors from PSI-MI 2.5 files
availableXrefs-methodsMethods for function availableXrefs
baitExtract bait, prey, participant, inhibitor, pubmed,...
BIOGRID.PSIMI25Supported PSI-MI 2.5 XML data sources
buildPCHypergraphBuild protein complex hypergraph from PSI-MI 2.5 files
complexesExtract complexes from psimi25ComplexEntry
complexNameAccessor functions for complex
eListHandlerxmlEventParse handlers for PSI-MI XML documents
getAbstractByPMIDA function to obtain the abstract information via a Pubmed ID
graphSpeciesConvertermaps one type of grap onto another
interactionsList interactions in the given psimi25InteractionEntry object
interactionTypeType of the interaction
interactorInfoInteractor info in a matrix
interactorInfo-methodsMethods for Function interactorInfo in Package 'RpsiXML'
interactorsGet information of interactors of the given object
list2MatrixConverts list into matrix
null2naTurns null or NA into character "NA"
numInteractions-methodsGet interaction number of the given object
parsePsimi25InteractionParsing PSI-MI 2.5 XML documents into interactions
psimi25Attribute-classClass "psimi25Attribute"
psimi25Complex-classClass "psimi25Complex"
psimi25ComplexEntry-classClass "psimi25ComplexEntry"
psimi25Experiment-classClass "psimi25Experiment"
psimi25Graph-classClass "psimi25Graph" ~~~
psimi25Hypergraph2GraphNELConvert psimi25Hypergraph to graphNEL
psimi25Hypergraph-classClass "psimi25Hypergraph"
psimi25Interaction-classClass "psimi25Interaction"
psimi25InteractionEntry-classClass "psimi25InteractionEntry"
psimi25Interactor-classA class representing interactor from PSI-MI 2.5 XML files
psimi25Source-classClass "psimi25Source"
psimi25XML2GraphConvert a vector of PSI-MI 2.5 XML files into graph objects
separateXMLDataByExptConvert a vector of PSI-MI 2.5 XML files into graph objects...
sourceId-methodsExtract or set source database name or ID in the source...
taxId-methodsGet or Set the NCBI Taxonomy ID or Organism Name
translateIDFinds identifiers of a given object
translateID-methodsTranslate interactors into other identifiers
uniprotThe UniProt Identifier in the PSI-MI 2.5 XML file
uniprot-methodsMethods for Function uniprot in Package 'RpsiXML'
validatePSIMI25Validating PSI-MI 2.5 file with MIF25 XML schema
alyst/RpsiXML documentation built on July 10, 2017, 11:46 p.m.