localNullModel {netboxr}R Documentation

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

netboxGraph

igraph network graph object. This igraph object contains NetBox algorithm identified network from geneConnector function

iterations

numeric value for number of iterations

Value

a list of returned results

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)


[Package netboxr version 1.2.0 Index]