getReactions

getReactions-methods

getReactions,KEGGPathway-method

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
 <code><a rd-options="" href="/link/KEGGPathway-class?package=KEGGgraph&version=1.30.0" data-mini-rdoc="KEGGgraph::KEGGPathway-class">KEGGPathway-class</a></code>, and the reactions elements are
 saved as a slot of the object, which can be retrieved with the
 function <code>getReactions</code>. 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 <code>KEGGPathway-class</code> object may have reactions
 information.

methods

KEGGGraph is an interface between KEGG pathway and graph
object as well as a collection of tools to analyze, dissect and
visualize these graphs. It parses the regularly updated KGML
(KEGG XML) files into graph models maintaining all essential
pathway attributes. The package offers functionalities
including parsing, graph operation, visualization and etc.

Jitao David Zhang

KEGGgraph

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

getReactions-methods function

<dl>
<dt>object = "KEGGPathway"</dt><dd> An object of <code><a rd-options="" href="/link/KEGGPathway-class?package=KEGGgraph&version=1.30.0" data-mini-rdoc="KEGGgraph::KEGGPathway-class">KEGGPathway-class</a></code></dd> </dl>

Methods

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
 <code><a href="KEGGPathway-class" rd-options="">KEGGPathway-class</a></code>, and the reactions elements are
 saved as a slot of the object, which can be retrieved with the
 function <code>getReactions</code>.

 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 <code>KEGGPathway-class</code> object may have reactions
 information.

getReactions-methods: Get KEGG reactions

Description

Arguments

Methods

References

See Also

Examples