getDisplayName-methods: Get a character string as label for display

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

Description

In KGML files, 'graph' element has a 'name' attribute to store the displaying name of a node, which is straighforward for end users. For example, biologists have no idea about a node 'hsa:1432' but its display name 'MAPK14' helps them to link this node to their knowledge. This method extract DisplayName from graph objects for KEGGNode and graph, where the method for graph returns the display names of its nodes.

Methods

object = "KEGGNode"

An object of KEGGNode-class

object = "graph"

A KEGG graph object

Author(s)

Jitao David Zhang mailto:[e-mail]

References

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

Examples

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

nodes <- nodes(pathway)
subnodes <- nodes[10:15]

sapply(subnodes, getDisplayName)
## compare them with getName, one 'displayName' may correspond to many paralogues
sapply(subnodes, getName)

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