KEGGNode-class: Class "KEGGNode"

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

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:[e-mail]

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)

Example output

Attaching package: 'KEGGgraph'

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

    plot

KEGG Node (Entry '1'):
------------------------------------------------------------
[ displayName ]: C00338
[ Name ]: cpd:C00338
[ Type ]: compound
[ Link ]: http://www.genome.jp/dbget-bin/www_bget?compound+C00338
------------------------------------------------------------
[1] "cpd:C00338"
[1] "C00338"
[1] "1"
[1] "C00338"

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