Class "Pathway"

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Description

A biological pathway.

Slots

id:

the native ID of the pathway.

title:

the title of the pathway.

edges:

a data.frame describing the edges of this pathway.

database:

the name of the database the pathway was derived from.

species:

the name of the species in which the pathway was annotated.

identifier:

the type of node identifier used by this pathway.

timestamp:

the date in which the pathway data was retrieved.

Methods

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 clipper analysis over the pathway.

runDEGraph(p, expr, classes, ...) Runs a DEGraph analysis over the pathway.

runTopologyGSA(p, test, exp1, exp2, alpha, ...) Runs a topologyGSA analysis over the pathway.

Author(s)

Gabriele Sales

See Also

pathways