aracne.net {minet} | R Documentation |
The Aracne algorithm applies the data processing inequality to all triplets of nodes in order to remove the least significant edge in each triplet.
aracne.net( mim, eps=0 )
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. |
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
.
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") )
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.
data(syn.data) mim <- build.mim(disc(syn.data)) net <- aracne.net(mim)