preparePathways: Prepare pathway dataset needed by NetGSA

In drjingma/netgsa: Network-Based Gene Set Analysis

Description

Prepare pathway dataset needed by NetGSA. See NetGSA for more details.

Usage

preparePathways(db=c("kegg", "MSigDB"), 
           type=c("H","C1","C2","C3","C4","C5","C6","C7"),
           genename= c("EntrezID", "symbol"))

Arguments

db	Database to build pathway from. Could be either 'kegg' or 'MSigDB'.
type	The type of pathways to choose from if db=='MSigDB'.
genename	Whether gene symbol or EntrezID is used.

Value

A list of pathways.

Author(s)

Jing Ma ([e-mail])

See Also

NetGSA

Examples

#library(graphite)

#pathwayList <- preparePathways('kegg')
#pathwayList[[1]]

drjingma/netgsa documentation built on Feb. 22, 2022, 5:18 p.m.