dna (version 2.1-2)

network.modules: Determine modules for network

Description

Determine the modular structure for a network.

Usage

network.modules(s,m,epsilon,plot=FALSE,interactive=FALSE,...)

Arguments

s

scores for a network.

m

minimum cluster size parameter.

epsilon

threshold parameter.

plot

indicates whether to create a graph for the network using the tkplot function in the igraph package.

interactive

indicates whether any plotted graphs should be interactive.

...

additional arguments passed to the tkplot function in the igraph package.

Value

modules

an object of S4-class "modules" for the network

References

Gill, R., Datta, S., and Datta, S. (2010) A statistical framework for differential network analysis from microarray data. BMC Bioinformatics, 11, 95.

Examples

# NOT RUN {
# artificial example to show how to obtain modules from a matrix of
# connectivity scores
set.seed(26)
s=matrix(runif(100,-1,1),10,10);diag(s)=1;s=round((s+t(s))/2,1)
the.modules=network.modules(s,m=3,epsilon=.7)
the.modules
# }