getKEGGPathway: Download KEGG pathway

In rags2ridges: Ridge Estimation of Precision Matrices from High-Dimensional Data

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:".

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

Value

Returns a list with entries:

df	A data.frame description of the KEGG pathway.
graph	The KEGG pathway represented as a graphNEL object.

Note

It is currently necessary to require("KEGGgraph") (or require("KEGGgraph")) due to a bug in KEGGgraph.

Author(s)

Anders Ellern Bilgrau, Carel F.W. Peeters <[e-mail]>, Wessel N. van Wieringen

References

https://www.genome.jp/kegg/

See Also

kegg.target

Examples

## Not run: 
if (require("KEGGgraph")) {
  getKEGGPathway("map04064")
}

## End(Not run)

rags2ridges documentation built on Oct. 14, 2023, 5:06 p.m.