KEGGPathway-class {KEGGgraph} | R Documentation

## 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:j.zhang@dkfz.de

### 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)

[Package KEGGgraph version 1.1.0 Index]