Class "DeprecatedPathwayList"

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Description

Represents deprecated objects for accessing pathway databases.

Extends

Class "Pathways", directly.

Methods

l[i]: Returns a selection of the pathways contained in the pathway list.

l[[i]] Access one of the pathways contained in the pathway list.

l$`title` Access one of the pathways by its title.

convertIdentifiers(l, to) Returns a new list of pathways using a different type of node identifiers.

length(l) Returns the number of pathways contained in the list.

names(l) Returns the titles of the pathways contained in the list.

prepareSPIA(l, pathwaySetName, print.names=FALSE) Prepares the pathways for a SPIA analysis.

runClipper(l, expr, classes, method, maxNodes=150, ...) Runs a clipper analysis over all the pathways in the list.

runDEGraph(l, expr, classes, maxNodes=150, ...) Runs a DEGraph analysis over all the pathways in the list.

runTopologyGSA(l, test, exp1, exp2, alpha, maxNodes=150, ...) Runs a topologyGSA analysis over all the pathways in the list.

Author(s)

Gabriele Sales

See Also

PathwayList