PartitionDensity: Illustration of partition density

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

Description

Calculate the average density of all resulting modules from a partition. The density of each module is defined as the average adjacency of the module genes.

Usage

PartitionDensity(ADJ, PartitionSet)

Arguments

ADJ	gene similarity matrix
PartitionSet	vector indicates the partition label for genes

Value

partition density, defined as average density of all modules

Author(s)

Dong Li, [e-mail]

References

Langfelder, Peter, and Steve Horvath. "WGCNA: an R package for weighted correlation network analysis." BMC bioinformatics 9.1 (2008): 1.

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 <- PartitionDensity(ADJ1,groups) 

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