subGraphByNodeType: Subset KEGG graph by node types
In Accio/KEGGgraph: KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor
subGraphByNodeType R Documentation
Subset KEGG graph by node types
Description
The function subsets KEGG graph by node types, mostly used in
extracting gene networks.
Usage
subGraphByNodeType(graph, type = "gene", kegg=TRUE)
Arguments
graph
A KEGG graph object produced by calling parseKGML2Graph
type
node type, see KEGGNodeType for details
kegg
logical, should the KEGG Node and Edge attributes be
maintained during the subsetting? By default set to 'TRUE'
Value
A subgraph of the original graph
Author(s)
Jitao David Zhang mailto:jitao_david.zhang@roche.com
Examples
sfile <- system.file("extdata/hsa04010.xml",package="KEGGgraph")
sGraph <- parseKGML2Graph(sfile,expandGenes=TRUE, genesOnly=FALSE)
sGraphGene <- subGraphByNodeType(sGraph, type="gene")
Accio/KEGGgraph documentation built on Jan. 13, 2023, 1:03 p.m.
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| subGraphByNodeType | R Documentation |
Subset KEGG graph by node types
Description
The function subsets KEGG graph by node types, mostly used in extracting gene networks.
Usage
subGraphByNodeType(graph, type = "gene", kegg=TRUE)
Arguments
graph |
A KEGG graph object produced by calling |
type |
node type, see |
kegg |
logical, should the KEGG Node and Edge attributes be maintained during the subsetting? By default set to 'TRUE' |
Value
A subgraph of the original graph
Author(s)
Jitao David Zhang mailto:jitao_david.zhang@roche.com
Examples
sfile <- system.file("extdata/hsa04010.xml",package="KEGGgraph")
sGraph <- parseKGML2Graph(sfile,expandGenes=TRUE, genesOnly=FALSE)
sGraphGene <- subGraphByNodeType(sGraph, type="gene")
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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