PathwayList-class: Class '"PathwayList"'

In sales-lab/graphite: GRAPH Interaction from pathway Topological Environment

Class "PathwayList"

Description

A collection of pathways from a single database.

Extends

Class "Pathways", directly.

Methods

l[i]

returns a selection of the pathways contained in the pathway list.

l[[i]]

gives access to one of the pathways contained in the pathway list.

l$`title`

loads a 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.

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

pathways

sales-lab/graphite documentation built on June 13, 2025, 3:20 a.m.