Class "KEGGPathway"

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:jitao_david.zhang@roche.com

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)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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Type 'demo()' for some demos, 'help()' for on-line help, or
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> library(KEGGgraph)

Attaching package: 'KEGGgraph'

The following object is masked from 'package:graphics':

    plot

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/KEGGgraph/KEGGPathway-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: KEGGPathway-class
> ### Title: Class "KEGGPathway"
> ### Aliases: KEGGPathway-class edges,KEGGPathway,ANY-method edges<-
> ###   edges<-,KEGGPathway-method getName,KEGGPathway-method
> ###   getTitle,KEGGPathway-method nodes<-,KEGGPathway,ANY-method
> ###   nodes,KEGGPathway-method edges,KEGGPathway-method
> ###   show,KEGGPathway-method getTitle,KEGGPathway-method
> ### Keywords: classes
> 
> ### ** 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
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)
------------------------------------------------------------
> 
> ## get information of the pathway
> getPathwayInfo(maptest)
[ 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
> 
> ## nodes of the pathway
> nodes <- nodes(maptest)
> node <- nodes[[3]]
> getName(node)
[1] "cpd:C16432"
> getType(node)
[1] "compound"
> getDisplayName(node)
[1] "C16432"
> 
> ## edges of the pathway
> edges <- edges(maptest)
> edge <- edges[[3]]
> getEntryID(edge)
Entry1ID Entry2ID 
    "17"     "81" 
> getSubtype(edge)
$subtype
  [ Subtype name ]: compound
  [ Subtype value ]: 96

> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>