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### TFA.estimate.R (2005-04-11)
###
### Prediction of Transcription Factor Activities using PLS
###
### Copyright 2004-04 Anne-Laure Boulesteix and Korbinian Strimmer
###
###
###
###
### This file is part of the `plsgenomics' library for R and related languages.
### It is made available under the terms of the GNU General Public
### License, version 2, or at your option, any later version,
### incorporated herein by reference.
###
### 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.
###
### You should have received a copy of the GNU General Public
### License along with this program; if not, write to the Free
### Software Foundation, Inc., 59 Temple Place - Suite 330, Boston,
### MA 02111-1307, USA
TFA.estimate<-function(CONNECdata,GEdata,ncomp=NULL,nruncv=0,alpha=2/3,unit.weights=TRUE)
{
n<-nrow(GEdata)
m<-ncol(GEdata)
p<-ncol(CONNECdata)
if (nruncv==0&length(ncomp)>1)
stop("Since length(ncomp)>1, nruncv must be >0")
if (is.null(ncomp))
{
ncomp<-min(n,p)
}
if (n!=nrow(CONNECdata))
stop("The number of genes must be the same in the gene expression data and in the CONNEC data")
X<-scale(CONNECdata,center=TRUE,scale=TRUE)
X[is.na(X)]<-0
Y<-scale(GEdata,center=TRUE,scale=TRUE)
if (nruncv>0)
{
ncomp<-pls.regression.cv(X,Y,ncomp=ncomp,nruncv=nruncv)
}
Dx<-diag(1/attributes(X)$"scaled:scale")
Dy<-diag(1/attributes(Y)$"scaled:scale")
pls.out<-pls.regression(X,Y,ncomp=ncomp,Xtest=NULL,unit.weights=unit.weights)
TFA<-Dx%*%pls.out$B%*%solve(Dy)
metafactor<-pls.out$Q
return(list(TFA=TFA,metafactor=metafactor,ncomp=ncomp))
}
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