library(AnnotationDbi)
directory <- system.file("/extdata/psi25files",
package="RpsiXML")
mintXML <- file.path(directory,
"mint_200711_test.xml")
mintGraph <- separateXMLDataByExpt(xmlFiles=mintXML,
psimi25source = MINT.PSIMI25,
type = "indirect",
directed=TRUE,
abstract=FALSE)
#
# if(require("hom.Mm.inp.db") & require("org.Mm.eg.db")) {
# newGraph = graphConverter(mintGraph[[1]], "MUSMU", "HOMSA")
# }
##Get a hypergraph
xmlDir <- system.file("/extdata/psi25files",package="RpsiXML")
intactComplexxml <- file.path(xmlDir,"intact_complexSample.xml")
hyperGraph <- buildPCHypergraph(intactComplexxml, INTACT.PSIMI25)
# if(require("hom.Hs.inp.db")) {
# ##Convert it
# newHyper = hyperGraphConverter(hyperGraph, "HOMSA", "MUSMU", "UNIPROT",
# "UNIPROT")
# }
##Get a incidence matrix from ScISI
if(require(ScISI))
data(ScISIC)
# if(require("org.Sc.eg.db")) {
# ##Convert it
# newScISIC = hyperGraphConverter(ScISIC, "SACCE", "MUSMU",
# srcIDType="ORF", destIDType = "EG")
# }
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