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# file dna/R/get.common.networks-methods.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/
#
setMethod("get.common.networks","pairOfNetworks",
function(object){
N1=slot(object,"network1")
N2=slot(object,"network2")
if ((!is.null(colnames(N1)))&(!is.null(colnames(N2)))){
common.genes=intersect(colnames(N1),colnames(N2))
iN1=match(common.genes,colnames(N1))
iN2=match(common.genes,colnames(N2))
network1=N1[,iN1]
network2=N2[,iN2]
}
else{
network1=N1
network2=N2
p=ncol(N1)
colnames(network1)=paste("Gene",1:p)
colnames(network2)=paste("Gene",1:p)
}
return(list(network1=network1,network2=network2))
})
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