getKcSubGraph {SubpathwayMiner}R Documentation

Mine sub-pathways

Description

Mine sub-pathways by using the k-clique concept in social network analysis.

Usage

     getKcSubGraph(k=4,graphList=getDefaultUndirectedGraph())

Arguments

k An integer. A distance similarity parameter.
graphList An undirected graph list. Detailed information is provided in uGraph or KOuGraph.

Details

The function uses the k-clique concept in social network analysis to mine sub-pathways. In social network analysis, a k-clique in a graph is a subgraph where the distance between any two nodes is no greater than k.

The default value of the argument graphList is obtained from the function getDefaultUndirectedGraph. It means to mine sub-pathways based on enzyme commission (EC) numbers from the version of metabolic pathways. If users hope to mine sub-pathways based on KEGG Orthology (KO), the value of graphList should be changed with the function getDefaultKOUndirectedGraph.

Value

A list of graphs.

Author(s)

Chunquan Li <lcqbio@yahoo.com.cn>

References

Wasserman,S. and Faust,K. (1994) Social network analysis: methods and applications. Cambridge University Press., New York, America.

Huber,W., Carey,V.J., Long,L., Falcon,S. and Gentleman,R. (2007) Graphs in molecular biology. BMC Bioinformatics., 8, s8.

See Also

getAnn,getKOAnn,getKcsmpAnn

Examples

##get graph representation of metabolic pathways
 graphList<-getDefaultUndirectedGraph()
#get all 4-clique subgraphs
 subGraphList<-getKcSubGraph(k=4,graphList)
#display first subGraph 
 library(Rgraphviz)
 plot(subGraphList[[1]])

##annotate a set of genes to the sub-pathways of metabolic pathways by using enzyme commission (EC) numbers.
geneList<-getAexample(k=1000)
subGraphList<-getKcSubGraph(k=4)
ann<-getAnn(geneList,graphList=subGraphList)
printAnn(ann)

##annotate the genes to sub-pathway by using KEGG Orthology (KO).
geneList<-getAexample(k=100)
subGraphList<-getKcSubGraph(k=4,graphList=getDefaultKOUndirectedGraph())
ann<-getKOAnn(geneList,graphList=subGraphList)
printAnn(ann)[2:5]


[Package SubpathwayMiner version 2.0 Index]