rags2ridges (version 2.2.2)

getKEGGPathway: Download KEGG pathway

Description

Download information and graph object of a given pathway from the Kyoto Encyclopedia of Genes and Genomes (KEGG) database.

Usage

getKEGGPathway(kegg.id)

Arguments

kegg.id

A character giving the KEGG ID, e.g. "map04210", "map04064", "map04115". Can be prefixed with "path:".

Value

Returns a list with entries:

df

A data.frame description of the KEGG pathway.

graph

The KEGG pathway represented as a graphNEL object.

Details

Usage of this function requires an internet connection. The igraph objects can be obtained with igraph::igraph.from.graphNEL. The moral graph can be obtained with gRbase::moralize. To obtain the adjacency matrix, use gRbase::as.adjMAT or igraph::get.adjacency

References

http://www.genome.jp/kegg/

See Also

kegg.target

Examples

# NOT RUN {
if (require("KEGGgraph")) {
  getKEGGPathway("map04064")
}
# }