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