localNullModel: Generate local null model p-value

In mil2041/netboxr: netboxr

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, [e-mail]

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)

mil2041/netboxr documentation built on May 20, 2023, 6:02 a.m.