getReactions-methods: Get KEGG reactions

In KEGGgraph: KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor

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:[e-mail]

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]

Example output

Attaching package: 'KEGGgraph'

The following object is masked from 'package:graphics':

    plot

KEGG Pathway
[ Title ]: Glycine, serine and threonine metabolism
[ Name ]: path:map00260
[ Organism ]: map
[ Number ] :00260
[ Image ] :http://www.genome.jp/kegg/pathway/map/map00260.gif
[ Link ] :http://www.genome.jp/dbget-bin/show_pathway?map00260
------------------------------------------------------------
Statistics:
	144 node(s)
	371 edge(s)
	68 reaction(s)
------------------------------------------------------------
$reaction
KEGG Reaction(rn:R08211)
------------------------------------------------------------
[ Name ]: rn:R08211
[ Type ]: irreversible
[ Substrate Name ]: cpd:C00576
[ Product Name ]: cpd:C00719

$reaction
KEGG Reaction(rn:R00589)
------------------------------------------------------------
[ Name ]: rn:R00589
[ Type ]: reversible
[ Substrate Name ]: cpd:C00065
[ Product Name ]: cpd:C00740

$reaction
KEGG Reaction(rn:R08050)
------------------------------------------------------------
[ Name ]: rn:R08050
[ Type ]: irreversible
[ Substrate Name ]: cpd:C06231
[ Product Name ]: cpd:C16432

KEGGgraph documentation built on Nov. 8, 2020, 5:42 p.m.