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# file dna/R/gennet.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/
#
gennet=function (data, f, recenter.data=FALSE, rescale.data=FALSE,
symmetrize.scores=FALSE, rescale.scores=FALSE, ...)
{
gene.names = colnames(data)
data=t(as.matrix(data))
data=scale(t(data),center=recenter.data,scale=rescale.data)
n = ncol(data)
if (is.null(gene.names))
gene.names = paste("Gene", 1:n)
s = matrix(0, n, n)
rownames(s) = gene.names
colnames(s) = gene.names
for (i in 1:n) {
X = data[, -i]
y = data[, i]
s[i, i] = 1 - rescale.scores
s[i, -i] = f(X, y, ...)
}
if (symmetrize.scores==TRUE)
s=0.5*(s+t(s))
if (rescale.scores==TRUE){
ss=max(abs(s))
diag(s)=rep(ss,length(diag(s)))
s=s/ss
}
s
}
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