subKEGGgraph {KEGGgraph} | R Documentation

## Subset KEGG graph, including subsetting node and edge attributes

### Description

`subKEGGgraph` extends generic method `subGraph` and subsets the KEGG graph. Both 'subKEGGgraph' and 'subGraph' can be used to subset the graph, the difference lies in whether the node and edge attributes from KEGG are also subset (`subKEGGgraph`) or not (`subGraph`).

See details below.

### Usage

    subKEGGgraph(nodes, graph)

### Arguments

`nodes` | Node names to subset
`graph` | A graph parsed from KGML files, produced by `parseKGML2Graph`, `KEGGpathway2Graph` or `parseKGMLexpandMaps`

### Details

`subGraph` does not subset the node or edge attributes, hence the results of `getKEGGnodeData` and `getKEGGedgeData` does not map to the nodes and edges in the subgraph in a one-to-one manner, with attributes of removed nodes and edges still remaining in the subGraph.

`subKEGGgraph` calls `subGraph` first to subset the graph, and then it also subsets the KEGGnodeData and KEGGedgeData so that they are one-to-one mapped to the nodes and edges in the subgraph.

### Value

A graph with nodeData and edgeData.

### Author(s)

Jitao David Zhang mailto:jitao_david.zhang@roche.com

### Examples

    sfile <- system.file("extdata/hsa04010.xml",package="KEGGgraph")
    gR <- parseKGML2Graph(sfile,expandGenes=TRUE)
    subs <-  c("hsa:1432",edges(gR)$`hsa:1432`,"hsa:5778","hsa:5801",
    "hsa:84867","hsa:11072","hsa:5606","hsa:5608","hsa:5494","hsa:5609")
    gR.keggsub <- subKEGGgraph(subs, gR)
    gR
    gR.keggsub

[Package KEGGgraph version 1.40.0 Index]