A biological pathway.
the native ID of the pathway.
the title of the pathway.
a data.frame describing the edges of this pathway.
the name of the database the pathway was derived from.
the name of the species in which the pathway was annotated.
the type of node identifier used by this pathway.
the date in which the pathway data was retrieved.
convertIdentifiers(p, to)Returns a new pathway using a different type of node identifiers.
edges(p)Returns a data.frame describing the edges of this pathway.
nodes(p)Return the names of the nodes belonging to this pathway.
plot(p)Shows the pathway topology in Cytoscape.
runClipper(p, expr, classes, method, ...)Runs a
clipperanalysis over the pathway.
runDEGraph(p, expr, classes, ...)Runs a
DEGraphanalysis over the pathway.
runTopologyGSA(p, test, exp1, exp2, alpha, ...)Runs a
topologyGSAanalysis over the pathway.
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