getKcSubGraph {SubpathwayMiner} | R Documentation |
Mine sub-pathways by using the k-clique concept in social network analysis.
getKcSubGraph(k=4,graphList=getDefaultUndirectedGraph())
k |
An integer. A distance similarity parameter. |
graphList |
An undirected graph list. Detailed information is provided in uGraph or KOuGraph . |
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
.
A list of graphs.
Chunquan Li <lcqbio@yahoo.com.cn>
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.
##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]