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# file dna/R/cornet.R
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 or 3 of the License
# (at your option).
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# A copy of the GNU General Public License is available at
# http://www.r-project.org/Licenses/
#
cornet = function(data,rescale.scores=FALSE){
data=as.matrix(data)
n=as.integer(nrow(data))
p=as.integer(ncol(data))
pp=as.integer(p*p)
gene.names=colnames(data)
if (is.null(gene.names))
gene.names=paste("Gene",1:p)
out=.C("rcor",as.double(data),s=double(pp),n,p)
s=matrix(out$s,p,p,byrow=FALSE)
rownames(s)=gene.names
colnames(s)=gene.names
if (rescale.scores==TRUE){
for (i in 1:p)
s[i,i]=0
ss=max(abs(s))
diag(s)=rep(ss,length(diag(s)))
s=s/ss
for (i in 1:p)
s[i,i]=1
}
s
}
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