findFinalClassifier-methods {magpie} | R Documentation |
This method generates and stores the final classifier corresponding
to an experiment. This classifier can then be used to classify new samples by
calling classifyNewSamples
. The final classifier is build according to the
classifier selected for a given experiment, applied on the whole data considering
only the genes selected by the feature selction method selected.
The methods returns an object of class experiment which finalClassifier has been build.
#dataPath <- file.path("C:", "Documents and Settings", "c.maumet", "My Documents", "Programmation", "Sources", "SVN", "R package", "data") #aDataset <- new("dataset", dataId="vantVeer_70", dataPath=dataPath) #aDataset <- loadData(aDataset) data('vV70genesDataset') # With the RFE-SVM as feature selection method expeOfInterest <- new("experiment", dataset=vV70genes, noFolds1stLayer=10, noFolds2ndLayer=9, classifierName="svm", typeFoldCreation="original", svmKernel="linear", noOfRepeat=2, featureSelectionOptions=new("geneSubsets", optionValues=c(1,2,4,8,16,32,64,70))) # Build the final classifier expeOfInterest <- findFinalClassifier(expeOfInterest) # With the NSC as feature selection method expeOfInterest <- new("experiment", dataset=vV70genes, noFolds1stLayer=10, noFolds2ndLayer=9, featureSelectionMethod="nsc", classifierName="nsc", typeFoldCreation="original", svmKernel="linear", noOfRepeat=2, featureSelectionOptions=new("thresholds")) # Build the final classifier expeOfInterest <- findFinalClassifier(expeOfInterest)