localNullModel {netboxr} | R Documentation |
This function keeps the number of connections of each nodes in the graph but it rewires the partners of connections and produces modularity score. When it repeats multiple time, a modularity score distribution will be used to produce netbox loacl p-value.
localNullModel(netboxGraph, iterations = 30)
netboxGraph |
igraph network graph object. This igraph object contains
NetBox algorithm identified network from |
iterations |
numeric value for number of iterations |
a list of returned results
randomModularityScore: vector of modularity scores in the iterations of local re-wiring randomization process
randomMean: numeric value of mean of modularity scores in the iterations of local re-wiring randomization process
randomSD: numeric value of standard deviation of modularity scores in the iterations of local re-wiring randomization process
modularityScoreObs: numeric value of observed modularity score in the NetBox algorithm identified network
zScore: numeric value of z-score
pValueObs: numeric value of observed p-value
Eric Minwei Liu, emliu.research@gmail.com
data(netbox2010) sifNetwork<-netbox2010$network graphReduced <- networkSimplify(sifNetwork,directed = FALSE) geneList<-as.character(netbox2010$geneList) results<-geneConnector(geneList=geneList,networkGraph=graphReduced, pValueAdj='BH',pValueCutoff=0.05, communityMethod='lec',keepIsolatedNodes=FALSE) names(results) # Suggested 1000 iterations. # Use 10 interations in the exampel to save running time. localTest <- localNullModel(netboxGraph=results$netboxGraph, iterations=10)