prepGraphite {mogsa} | R Documentation

## 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".

### Details

Only support "entrez" or "symbol" output currently.

### 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".

### Author(s)

Chen Meng

### References

Sales G, Calura E and Romualdi C (2014). graphite: GRAPH Interaction from pathway Topological Environment. R package version 1.10.1.

### See Also

See Also as `prepMsigDB` and `prepSupMoa`.

### Examples

      library(graphite)
      keggdb <- prepGraphite(db = pathways("hsapiens", "kegg")[1:3], id = "entrez")

[Package mogsa version 1.26.0 Index]