R/get.common.networks-methods.R

In dna: Differential Network Analysis

# 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))
})