gsaPathwayGmt: Retrieve pathway genesets.

In bernau/survHDExtra: Addtitional Features for package survHD

Description

Provides the Biocarta, Reactome, KEGG and NCI pathway databases as geneset objects. Utilizes the graphite package.

Usage

    gsaPathwayGmt(pathway,type="symbol")

Arguments

pathway	Either a string with the pathway name (reactome, kegg, nci, biocarta) or a list of pathway objects as defined in the graphite package.
type	Genesets can bei either official gene symbols (default) or entrez ids.

Details

Provides quick access to the main pathway databases.

Value

An object of class gsagenesets.

Author(s)

[e-mail], Levi Waldron [e-mail], Christoph Bernau [e-mail]

See Also

gsaWilcoxSurv, gsaReadGmt

Examples

## Not run: 
    require(survHDExtra)
    gmt.reactome <- gsaPathwayGmt("reactome")
    
## End(Not run)

bernau/survHDExtra documentation built on May 12, 2019, 4:22 p.m.