rags2ridges: getKEGGPathway – R documentation

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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:".

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 <cf.peeters@vumc.nl>, Wessel N. van Wieringen

References

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

Examples

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

## End(Not run)

rags2ridges

Ridge Estimation of Precision Matrices from High-Dimensional Data

v2.2.4

GPL (>= 2)

Authors

Carel F.W. Peeters [cre, aut], Anders Ellern Bilgrau [aut], Wessel N. van Wieringen [aut]

Initial release