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### Class prediction based on PLS dimension reduction (without pre-validation) and random forests
### with microarray data only
###
### Copyright 2007-11 Anne-Laure Boulesteix
###
###
###
###
### This file is part of the `MAclinical' 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
plsrf_x<-function(Xlearn,Zlearn=NULL,Ylearn,Xtest,Ztest=NULL,ncomp=0:3,ordered=NULL,nbgene=NULL,...)
{
ncomp<-ncomp[ncomp!=0]
Ylearn<-as.numeric(factor(Ylearn))-1
nlearn<-length(Ylearn)
p<-ncol(Xlearn)
if (is.null(ordered)&is.null(nbgene))
{
ordered<-1:p
}
if (is.null(ordered)&!is.null(nbgene))
{
ordered<-order(abs(studentt.stat(X=Xlearn,L=Ylearn+1)),decreasing=TRUE)
}
if (is.null(nbgene))
{
nbgene<-p
}
output.pls<-pls.regression(Xlearn[,ordered[1:nbgene]],Ylearn+1,ncomp=max(ncomp))
XXlearn<-scale(Xlearn[,ordered[1:nbgene]],scale=FALSE,center=output.pls$meanX)%*%output.pls$R[,1:max(ncomp)]
XXtest<-matrix(scale(Xtest[,ordered[1:nbgene]],scale=FALSE,center=output.pls$meanX)%*%output.pls$R[,1:max(ncomp)],nrow=nrow(Xtest))
output.forest<-list()
OOB<-numeric(length(ncomp))
for (i in 1:length(ncomp))
{
data.learn<-data.frame(XXlearn[,1:ncomp[i]],y=factor(Ylearn))
data.test<-data.frame(XXtest[,1:ncomp[i]])
names(data.learn)<-c(sapply(as.list(1:ncomp[i]),FUN=paste,".comp"),"y")
names(data.test)<-sapply(as.list(1:ncomp[i]),FUN=paste,".comp")
output.forest[[i]]<-cforest(formula=y~.,data=data.learn,controls=cforest_control(ntree=200,mincriterion=qnorm(0.5),mtry=floor(sqrt(ncol(data.learn)-1)),replace=FALSE))
OOB[i]<-sum(predict(output.forest[[i]],OOB=TRUE)!=Ylearn)/nlearn
}
best<-which.min(OOB)
bestncomp<-ncomp[best]
output.forest<-output.forest[[best]]
importance<-varimp(output.forest)
newdata<-data.frame(data.test[,1:bestncomp])
names(newdata)<-sapply(as.list(1:bestncomp),FUN=paste,".comp")
prediction<-as.numeric(predict(object=output.forest,newdata=newdata))-1
return(list(prediction=prediction,importance=importance,bestncomp=bestncomp,OOB=OOB))
}
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