getReactions-methods {KEGGgraph} | R Documentation

## Get KEGG reactions

### Description

In KGML, the pathway element specifies one graph object with the entry elements as its nodes and the relation and reaction elements as its edges. The relation elements are saved as edges in objects of `KEGGPathway-class`, and the reactions elements are saved as a slot of the object, which can be retrieved with the function `getReactions`.

Regulatory pathways are always viewed as protein networks, so there is no 'reaction' information saved in their KGML files. Metabolic pathways are viewed both as both protein networks and chemical networks, hence the `KEGGPathway-class` object may have reactions information.

### Methods

object = "KEGGPathway"
  An object of `KEGGPathway-class`

### Author(s)

Jitao David Zhang mailto:j.zhang@dkfz.de

### References

KGML Document manual http://www.genome.jp/kegg/docs/xml/

### See Also

`KEGGPathway-class`

### Examples

    mapfile <- system.file("extdata/map00260.xml", package="KEGGgraph")
    maptest <- parseKGML(mapfile)
    maptest

    mapReactions <- getReactions(maptest)
    mapReactions[1:3]

[Package KEGGgraph version 1.1.0 Index]