Generate local null model p-value

Description

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.

Usage

localNullModel(netboxGraph, iterations = 30)

Arguments

Value

a list with four lists (i.e. netboxOutput, nodeType, moduleMembership, neighborData)

Author(s)

Eric Minwei Liu, emliu.research@gmail.com

Examples

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)