KEGGNode-class {KEGGgraph} | R Documentation

## Class "KEGGNode"

### Description

The class to present 'entry' element in KGML files and nodes in KEGG graphs

### Objects from the Class

Objects can be created by calls of the function `parseEntry` and is not intended to be directly created by users.

### Slots

`entryID`:

  entryID, the 'id' attribute of 'entry' elements in KGML files. In each KGML file the entryID is specified by auto-increment integers, therefore entryIDs from two individual KGML files are not unique. However, if 'expandGenes' option is specified in `KEGGpathway2Graph` function, the unique KEGGID will replace the default integer as the new entryID, which is unique in biological context

`name`:

  Name of the node

`type`:

  Type of the node, use `data(KEGGNodeType)` to see available values

`link`:

  URL link of the node

`reaction`:

  Reaction of the node

`map`:

  Map of the node

`graphics`:

  Graphic details (including display name) of the node, an object of `KEGGGraphics`

### Methods

getDisplayName

  `signature(object = "KEGGNode")`: get display name

getEntryID

  `signature(obj = "KEGGNode")`: get entryID, in case of gene-expanded graphs this is the same as getKEGGID

getKEGGID

  `signature(object = "KEGGNode")`: get KEGGID

getType

  `signature(object = "KEGGNode")`: get the type of the node

<-name

  `signature(object = "KEGGNode")`: replace name

getComponent

  `signature(obj = "KEGGNode")`: returns entryID (the same as `getEntryID`), for compatibility with `KEGGGroup-class`

show

  `signature(object = "KEGGNode")`: show 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

`KEGGEdge-class`, `parseEntry`

### Examples

    ## We show how to extract information from KEGGNode object
    sfile <- system.file("extdata/hsa04010.xml",package="KEGGgraph")
    pathway <- parseKGML(sfile)

    ns <- nodes(pathway)
    node <- ns[[1]]

    show(node)
    getName(node)
    getDisplayName(node)
    getEntryID(node)
    getKEGGID(node)

[Package KEGGgraph version 1.40.0 Index]