PartitionModularity {MODA}R Documentation

Illustration of modularity density

Description

Calculate the average modularity of a partition. The modularity of each module is defined from a natural generalization of unweighted case.

Usage

PartitionModularity(ADJ, PartitionSet)

Arguments

ADJ

gene similarity matrix

PartitionSet

vector indicates the partition label for genes

Value

partition modularity, defined as average modularity of all modules

Author(s)

Dong Li, dxl466@cs.bham.ac.uk

References

Newman, Mark EJ. "Analysis of weighted networks." Physical review E 70.5 (2004): 056131.

Examples

data(synthetic)
ADJ1=abs(cor(datExpr1,use="p"))^10
dissADJ=1-ADJ1
hierADJ=hclust(as.dist(dissADJ), method="average" )
groups <- cutree(hierADJ, h = 0.8)
pDensity <- PartitionModularity(ADJ1,groups) 


[Package MODA version 1.18.0 Index]