getName-methods: Get 'name' attribute

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

Get 'name' attribute

Description

Get 'name' attribute for given object, this method can be used for almost all objects implemented in KEGGgraph package to extract their name slot. See manual pages of individual objects for examples.

Methods

object = "KEGGEdgeSubType"

An object of KEGGEdgeSubType-class

object = "KEGGNode"

An object of KEGGNode-class

object = "KEGGPathway"

An object of KEGGPathway-class

object = "KEGGPathwayInfo"

An object of KEGGPathwayInfo-class

object = "KEGGReaction"

An object of KEGGReaction-class

Author(s)

Jitao David Zhang mailto:[e-mail]

References

KGML Document Manual https://www.genome.jp/kegg/docs/xml/

Examples

sfile <- system.file("extdata/hsa04010.xml",package="KEGGgraph")
pathway <- parseKGML(sfile)

## get pathway name
getName(pathway)

## get node name
nodes <- nodes(pathway)
getName(nodes[[2]])

## get edge name: it is not informative since the nodes are identified
## with file-dependent indices
edges <- edges(pathway)
getName(edges[[7]])

## get subtype name
subtype <- getSubtype(edges[[2]])[[1]]
getName(subtype)

Accio/KEGGgraph documentation built on Jan. 13, 2023, 1:03 p.m.