getKEGGnodeData: Get or set list of KEGG node or edge data

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

Description

The 'get' methods extracts KEGG node (edge) attributes from a graph produced by calling parseKGML2Graph or KEGGpathway2Graph. The 'set' methods writes a list into the edge or node data.

Usage

getKEGGnodeData(graph, n)
getKEGGedgeData(graph, n)

Arguments

graph	a graph object by parsing KGML file, where KEGG node and edge attributes are maintained
n	optional character string, name of the desired node or edge. If is missing all node Data is returned

Details

Node and edge data is stored as list within environments in graphs to save memory and speed up graph manipulations. When using getKEGGnodeData or getKEGGedgeData is called, the list is extracted out of the environment and returned.

Value

Either a list or single item of KEGGNode-class or KEGGEdge-class object(s).

Note

These functions will be unified into 'KEGGnodeData' and 'KEGGnodeData<-' forms.

Author(s)

Jitao David Zhang mailto:[e-mail]

Examples

sfile <- system.file("extdata/hsa04010.xml",package="KEGGgraph")
gR <- parseKGML2Graph(sfile,expandGenes=TRUE)
getKEGGnodeData(gR,"hsa:4214")
getKEGGedgeData(gR,"hsa:4214~hsa:5605")

Example output

Attaching package: 'KEGGgraph'

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

    plot

KEGG Node (Entry 'hsa:4214'):
------------------------------------------------------------
[ displayName ]: MAP3K1, MEKK1
[ Name ]: hsa:4214
[ Type ]: gene
[ Link ]: http://www.genome.jp/dbget-bin/www_bget?hsa+4214
------------------------------------------------------------
  KEGG Edge (Type: PPrel):
------------------------------------------------------------
[ Entry 1 ID ]: hsa:4214
[ Entry 2 ID ]: hsa:5605
[ Subtype ]: 
  [ Subtype name ]: phosphorylation
  [ Subtype value ]: +p
------------------------------------------------------------

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