KEGGpathway2reactionGraph {KEGGgraph} | R Documentation |
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 among chemical compounds.
This functions extracts reaction information from KEGG pathway, and convert the chemical compound reaction network into directed graph.
KEGGpathway2reactionGraph(pathway, uniqueReaction = TRUE)
pathway |
A KEGGPathway-class object, usually as the
result of the function parseKGML |
uniqueReaction |
logical, to indicate whether several chemical reactions (identified by different KEGG reaction ID) should be treated as one (TRUE) or many (FALSE) |
The direction of the graph is specified by the role of the compound in the reaction, the edges goes always out of 'substrate' and points to 'product'.
For now there is no wrapper to parse the KGML file directly into a
reaction graph. In future there maybe one, but we don't want to
confuse users with two similar functions to parse the file into a
graph (since we assume that most users will need the protein graph,
which can be conveniently parsed by parseKGML2Graph
).
A directed graph with compounds as nodes and reactions as edges.
Jitao David Zhang mailto:j.zhang@dkfz.de
KGML Document manual http://www.genome.jp/kegg/docs/xml/
mapfile <- system.file("extdata/map00260.xml",package="KEGGgraph") map <- parseKGML(mapfile) cg <- KEGGpathway2reactionGraph(map, uniqueReaction=FALSE) cg nodes(cg)[1:3] edges(cg)[1:3]