| KEGGPathway-class {KEGGgraph} | R Documentation |
A class to represent KEGG pathway
Objects can be created by calls of the form new("KEGGPathway",
...) . Normally they are created by parseKGML.
pathwayInfo:KEGGPathwayInfo-classnodes:KEGGNode-classedges:KEGGEdge-class reactions:KEGGReaction-class signature(object = "KEGGPathway", which =
"ANY"): KEGGEdges of the pathwaysignature(object = "KEGGPathway"): setting edgessignature(object = "KEGGPathway"): getting
pathway name signature(object = "KEGGPathway"): getting
pathway title signature(object = "KEGGPathway", value =
"ANY"): setting nodessignature(object = "KEGGPathway"): KEGGNodes of
the pathway signature(object = "KEGGPathway"): getting
KEGGPathwayInfosignature(object = "KEGGPathway"): getting
title of the pathway signature(object = "KEGGPathway"): display method Jitao David Zhang mailto:j.zhang@dkfz.de
KGML Document manual http://www.genome.jp/kegg/docs/xml/
parseKGML,
KEGGEdge-class, KEGGNode-class,
KEGGReaction-class
## We show how to extract information from KEGGPathway objects
## Parse KGML file into a 'KEGGPathway' object
mapfile <- system.file("extdata/map00260.xml", package="KEGGgraph")
maptest <- parseKGML(mapfile)
## short summary of the pathway
maptest
## get information of the pathway
getPathwayInfo(maptest)
## nodes of the pathway
nodes <- nodes(maptest)
node <- nodes[[3]]
getName(node)
getType(node)
getDisplayName(node)
## edges of the pathway
edges <- edges(maptest)
edge <- edges[[3]]
getEntryID(edge)
getSubtype(edge)