KEGGPathway-class: Class "KEGGPathway"

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

Description

A class to represent KEGG pathway

Objects from the Class

Objects can be created by calls of the form new("KEGGPathway", ...) . Normally they are created by parseKGML.

Slots

pathwayInfo:

An object of KEGGPathwayInfo-class

nodes:

List of objects of KEGGNode-class

edges:

List of objects of KEGGEdge-class

reactions:

List of objects of KEGGReaction-class

Methods

edges

signature(object = "KEGGPathway", which = "ANY"): KEGGEdges of the pathway

edges<-

signature(object = "KEGGPathway"): setting edges

getName

signature(object = "KEGGPathway"): getting pathway name

getTitle

signature(object = "KEGGPathway"): getting pathway title

nodes<-

signature(object = "KEGGPathway", value = "ANY"): setting nodes

nodes

signature(object = "KEGGPathway"): KEGGNodes of the pathway

getPathwayInfo

signature(object = "KEGGPathway"): getting KEGGPathwayInfo

getTitle

signature(object = "KEGGPathway"): getting title of the pathway

show

signature(object = "KEGGPathway"): display method

Author(s)

Jitao David Zhang mailto:[e-mail]

References

KGML Document manual http://www.genome.jp/kegg/docs/xml/

See Also

parseKGML, KEGGEdge-class, KEGGNode-class, KEGGReaction-class

Examples

## 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)

Example output

Attaching package: ‘KEGGgraph’

The following object is masked from ‘package:graphics’:

    plot

The following object is masked from ‘package:base’:

    plot

KEGG Pathway
[ Title ]: Glycine, serine and threonine metabolism
[ Name ]: path:map00260
[ Organism ]: map
[ Number ] :00260
[ Image ] :http://www.genome.jp/kegg/pathway/map/map00260.gif
[ Link ] :http://www.genome.jp/dbget-bin/show_pathway?map00260
------------------------------------------------------------
Statistics:
	144 node(s)
	371 edge(s)
	68 reaction(s)
------------------------------------------------------------
[ Title ]: Glycine, serine and threonine metabolism
[ Name ]: path:map00260
[ Organism ]: map
[ Number ] :00260
[ Image ] :http://www.genome.jp/kegg/pathway/map/map00260.gif
[ Link ] :http://www.genome.jp/dbget-bin/show_pathway?map00260
[1] "cpd:C16432"
[1] "compound"
[1] "C16432"
Entry1ID Entry2ID 
    "17"     "81" 
$subtype
  [ Subtype name ]: compound
  [ Subtype value ]: 96

KEGGgraph documentation built on Nov. 8, 2020, 5:42 p.m.