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#This file belongs to
#c3net: C3NET, <https://r-forge.r-project.org/projects/c3net/>
#This R package allows inferring regulatory networks from expression data using C3NET.
#The inferred network consists of only direct physical interactions.
## Copyright (C) January 2011 Gokmen Altay <altayscience@gmail.com>
## This program is a free software for only academic useage but not for commercial useage; you can redistribute it and/or
## modify it under the terms of the GNU GENERAL PUBLIC LICENSE
## either version 3 of the License, or any later version.
##
## This program is distributed WITHOUT ANY WARRANTY;
## You can get a copy of the GNU GENERAL PUBLIC LICENSE
## from
## http://www.gnu.org/licenses/gpl.html
## See the licence information for the dependent package from
## igraph package itself.
makemim <- function(expdata) # symetric MI matrix is input
{
gnames<-rownames(expdata)
txdata <-t(expdata)
genenum <- ncol(txdata)
rho2 <- cor(txdata)^2
for(irh in 1:genenum) for(jrh in 1:genenum)
{ if(rho2[irh,jrh]>=1) {rho2[irh,jrh] <- 0.9999999}
}
mim <- -0.5*log(1-rho2)
mim <- abs(mim)
diag(mim)<-0
rownames(mim) <-gnames
colnames(mim) <-gnames
mim
}
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