getReactions-methods | R Documentation |
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.
An object of KEGGPathway-class
Jitao David Zhang mailto:jitao_david.zhang@roche.com
KGML Document manual https://www.genome.jp/kegg/docs/xml/
KEGGPathway-class
mapfile <- system.file("extdata/map00260.xml", package="KEGGgraph") maptest <- parseKGML(mapfile) maptest mapReactions <- getReactions(maptest) mapReactions[1:3]
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