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-class
nodes
:KEGGNode-class
edges
: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)