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

- 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

### 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 1.7.1 Index]