getKcSubGraph {SubpathwayMiner}R Documentation

Mine sub-pathways from the version of metabolic pathways

Description

Mine sub-pathways from the version of metabolic 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.

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.

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,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
geneList<-getAexample(k=1000)
subGraphList<-getKcSubGraph(k=4)
ann<-getAnn(geneList,graphList=subGraphList)
printAnn(ann)


[Package SubpathwayMiner version 1.1 Index]