Description Objects from the Class Slots Methods References Examples
The class of modules of a network.
Objects can be created by calls of the form new("modules", ...)
.
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.
signature(object = "modules")
: lists the genes in each of the modules.
signature(x = "modules")
: summarizes a network by listing the number of genes in each module.
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.
Gill, R., Datta, S., and Datta, S. (2010) A statistical framework for differential network analysis from microarray data. BMC Bioinformatics, 11, 95.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 | # 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')
|
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