dna (version 2.1-2)

modules-class: Class "modules"

Description

The class of modules of a network.

Objects from the Class

Objects can be created by calls of the form new("modules", ...).

Slots

module:

Object of class "factor" which represents the module number of the genes in a network. For genes that are in none of the modules, the module number is listed as 0.

Methods

show

signature(object = "modules"): lists the genes in each of the modules.

summary

signature(x = "modules"): summarizes a network by listing the number of genes in each module.

get.modules

signature(object = "modules"): returns the module number for each gene in a network. For the genes that are in none of the modules, the module number is listed as 0.

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

# summary method useful for large networks
summary(the.modules)

# method for extracting the modules
get.modules(the.modules)

# plot a graph of the modules
## Not run: network.modules(s,m=3,epsilon=.7,plot=TRUE)
## Not run: tkplot.close('1')
# }