prepGraphite:
Prepare pathway gene sets from graphite package
Description
Prepare pathway gene sets from "graphite" package, which could be passed to "prepSupMoa" function.
Usage
prepGraphite(db, id = c("entrez", "symbol"))
Arguments
db
The database to be used, an object of class either 'PathwayList' create by "pathways" function.
id
Which identifier for output, either "entrez" or "symbol".
Value
This function returns an object of list containing gene set information, which could be further processed by function "prepSupMoa" to convert to the object that can be used as input of "sup.moa" or "mogsa".
Details
Only support "entrez" or "symbol" output currently.
References
Sales G, Calura E and Romualdi C (2014). graphite: GRAPH Interaction from pathway Topological Environment. R package version 1.10.1.