aracne.net {minet}R Documentation

Algorithm for the Reconstruction of Accurate Cellular NEtworks

Description

The Aracne algorithm applies the data processing inequality to all triplets of nodes in order to remove the least significant edge in each triplet.

Usage

aracne.net( mim, eps=0 )

Arguments

mim the mutual information matrix - see build.mim.
eps for each triplet of nodes (i,j,k), the weakest edge, say (ij), is removed if its weight is below min{(ik),(jk)}-eps - see references.

Details

The Aracne procedure starts by assigning to each pair of nodes a weight equal to their mutual information. Then, the weakest edge of each triplet is interpreted as an indirect interaction and is removed if the difference between the two lowest weights is above a threshold eps.

Value

aracne.net returns a matrix which is the weighted adjacency matrix of the network. In order to display the network, load the package Rgraphviz and use the following command:
plot( as( returned.matrix ,"graphNEL") )

References

Adam A. Margolin, Ilya Nemenman, Katia Basso, Chris Wiggins, Gustavo Stolovitzky, Riccardo Dalla Favera, and Andrea Califano. Aracne : An algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context. BMC Bioinformatics, 2006.

See Also

build.mim, clr.net, mr.net

Examples

data(syn.data)
mim <- build.mim(disc(syn.data))
net <- aracne.net(mim)

[Package minet version 1.1.3 Index]