PartitionModularity: Illustration of modularity density

In fairmiracle/MODA: MODA: MOdule Differential Analysis for weighted gene co-expression network

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, [e-mail]

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) 

fairmiracle/MODA documentation built on May 16, 2019, 9:59 a.m.