parsePsimi25Interaction {RpsiXML} | R Documentation |
The PSI-MI 2.5 XML format is used widely by many repositories to record protein-protein interaction data as well as protein complex data. This functions parse such files into interactions or complexes.
parsePsimi25Interaction
is the parser for interaction data and
parsePsimi25Complex
is the parser for complex data.
parsePsimi25Interaction(psimi25file, psimi25source, verbose=TRUE) parsePsimi25Complex(psimi25file, psimi25source, verbose=FALSE)
psimi25file |
character, file name or URL of the XML document |
psimi25source |
A supported data repository source, see also
psimi25Source-class |
verbose |
logical, whether the parsing state should be displayed verbosely. |
psimi25Interaction
returns a list of psimi25InteractionEntry
objects, each represents one entry
in the XML document
psimi25Complex
returns a psimi25ComplexEntry
objects,
representing the complex data from one XML document.
Jitao David Zhang <j.zhang@dkfz-heidelberg.de>, Tony Chiang <tchiang@ebi.ac.uk>
psimi25Interaction-class
,
psimi25InteractionEntry-class
,
psimi25Complex-class
psimi25ComplexEntry-class
,
# parse interaction data xmlDir <- system.file("/extdata/psi25files",package="RpsiXML") gridxml <- file.path(xmlDir, "biogrid_200804_test.xml") gridSet <- parsePsimi25Interaction(gridxml, BIOGRID.PSIMI25) intactxml <- file.path(xmlDir, "intact_2008_test.xml") intactSet <- parsePsimi25Interaction(intactxml, INTACT.PSIMI25, verbose=TRUE) # parse complex data intactComplexxml <- file.path(xmlDir,"intact_complexSample.xml") intactComplexSet <- parsePsimi25Complex(intactComplexxml, INTACT.PSIMI25)