prepGraphite: Prepare pathway gene sets from graphite package

Description Usage Arguments Details Value Author(s) References See Also Examples

View source: R/preGeneSet.R

Description

Prepare pathway gene sets from "graphite" package, which could be passed to "prepSupMoa" function.

Usage

1
    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

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2
  library(graphite)
  keggdb <- prepGraphite(db = pathways("hsapiens", "kegg")[1:3], id = "entrez")

mengchen18/mogsa documentation built on Nov. 23, 2017, 1:57 a.m.