PathwayList-class {graphite} | R Documentation

## 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]]` 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.

  `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`

[Package graphite version 1.26.3 Index]