Entry: classifyNewSamples-methods
Aliases: classifyNewSamples classifyNewSamples-methods classifyNewSamples,assessment-method
Keywords: methods
Description: classifyNewSamples Method to classify new samples for a given assessment
URL: ../../../library/Rmagpie/html/classifyNewSamples-methods.html

Entry: assessment-class
Aliases: assessment-class getClassifierName,assessment-method getClassifierName<-,assessment-method getClassifierName getClassifierName<- getFeatureSelectionMethod,assessment-method getNoFolds1stLayer,assessment-method getNoFolds1stLayer<-,assessment-method getNoFolds1stLayer getNoFolds1stLayer<- getNoFolds2ndLayer,assessment-method getNoFolds2ndLayer<-,assessment-method getNoFolds2ndLayer getNoFolds2ndLayer<- getNoOfRepeats,assessment-method getNoOfRepeats<-,assessment-method getNoOfRepeats getNoOfRepeats<- getResult1LayerCV,assessment-method getResult1LayerCV<-,assessment-method getResult1LayerCV getResult1LayerCV<- getResult2LayerCV,assessment-method getResult2LayerCV<-,assessment-method getResult2LayerCV getResult2LayerCV<- getSvmKernel,assessment-method getSvmKernel<-,assessment-method getSvmKernel getSvmKernel<- getTypeFoldCreation,assessment-method getTypeFoldCreation<-,assessment-method getTypeFoldCreation getTypeFoldCreation<-
Keywords: classes
Description: assessment: A central class to perform one and two layers of external cross-validation on microarray data
URL: ../../../library/Rmagpie/html/experiment-class.html

Entry: featureSelectionOptions-class
Aliases: featureSelectionOptions-class getOptionValues,featureSelectionOptions-method
Keywords: classes
Description: "featureSelectionOptions": A virtual class to store the options of a feature selection
URL: ../../../library/Rmagpie/html/featureSelectionOptions-class.html

Entry: finalClassifier-class
Aliases: finalClassifier-class getGenesFromBestToWorst,finalClassifier-method getGenesFromBestToWorst getModels,finalClassifier-method getModels
Keywords: classes
Description: finalClassifier: A class to store the final classifier corresponding to an assessment
URL: ../../../library/Rmagpie/html/finalClassifier-class.html

Entry: findFinalClassifier-methods
Aliases: findFinalClassifier findFinalClassifier-methods findFinalClassifier,assessment-method
Keywords: methods
Description: findFinalClassifier Method to train and build the final classifier based on an assessment
URL: ../../../library/Rmagpie/html/findFinalClassifier-methods.html

Entry: geneSubsets-class
Aliases: geneSubsets-class getMaxSubsetSize,geneSubsets-method getMaxSubsetSize<-,geneSubsets-method getMaxSubsetSize getMaxSubsetSize<- getNoModels,geneSubsets-method getNoModels getSpeed,geneSubsets-method getSpeed<-,geneSubsets-method getSpeed getSpeed<- getSubsetsSizes,geneSubsets-method getSubsetsSizes<-,geneSubsets-method getSubsetsSizes getSubsetsSizes<-
Keywords: classes
Description: geneSubsets: A class to handle the sizes of gene susbets to be tested during forward gene selection
URL: ../../../library/Rmagpie/html/geneSubsets-class.html

Entry: getDataset-methods
Aliases: getDataset-methods getDataset getDataset,assessment-method
Keywords: methods
Description: getDataset Method to access the attributes of a dataset from an assessment
URL: ../../../library/Rmagpie/html/getDataset-methods.html

Entry: getFeatureSelectionOptions-methods
Aliases: getFeatureSelectionOptions,assessment-method getFeatureSelectionOptions-methods getFeatureSelectionOptions
Keywords: methods
Description: getFeatureSelectionOptions Method to access the attributes of a featureSelectionOptions from an assessment
URL: ../../../library/Rmagpie/html/getFeatureSelectionOptions-methods.html

Entry: getFinalClassifier-methods
Aliases: getFinalClassifier,assessment-method getFinalClassifier-methods getFinalClassifier
Keywords: methods
Description: getFinalClassifier Method to access the attributes of a finalClassifier from an assessment
URL: ../../../library/Rmagpie/html/getFinalClassifier.html

Entry: getResults-methods
Aliases: getResults-methods getResults getResults,assessment-method
Keywords: methods
Description: getResults Method to access the result of one-layer and two-layers cross-validation from an assessment
URL: ../../../library/Rmagpie/html/getResults-methods.html

Entry: initialize-methods
Aliases: initialize,assessment-method initialize,geneSubsets-method initialize,thresholds-method
Keywords: methods
Description: Initialize objects of class from Rmagpie
URL: ../../../library/Rmagpie/html/initialize-methods.html

Entry: plotErrorsFoldTwoLayerCV-methods
Aliases: plotErrorsFoldTwoLayerCV plotErrorsFoldTwoLayerCV-methods plotErrorsFoldTwoLayerCV,assessment-method
Keywords: methods
Description: plotErrorsFoldTwoLayerCV Method to plot the error rate of a two-layer Cross-validation
URL: ../../../library/Rmagpie/html/plotErrorsFoldTwoLayerCV-methods.html

Entry: plotErrorsRepeatedOneLayerCV-methods
Aliases: plotErrorsRepeatedOneLayerCV plotErrorsRepeatedOneLayerCV-methods plotErrorsRepeatedOneLayerCV,assessment-method
Keywords: methods
Description: plotErrorsRepeatedOneLayerCV Method to plot the estimated error rates in each repeat of a one-layer Cross-validation
URL: ../../../library/Rmagpie/html/plotErrorsRepeatedOneLayerCV.html

Entry: plotErrorsSummaryOneLayerCV-methods
Aliases: plotErrorsSummaryOneLayerCV plotErrorsSummaryOneLayerCV-methods plotErrorsSummaryOneLayerCV,assessment-method
Keywords: methods
Description: plotErrorsSummaryOneLayerCV Method to plot the summary estimated error rates of a one-layer Cross-validation
URL: ../../../library/Rmagpie/html/plotErrorsSummaryOneLayerCV-methods.html

Entry: rankedGenesImg-methods
Aliases: rankedGenesImg rankedGenesImg-methods rankedGenesImg,assessment-method
Keywords: methods
Description: rankedGenesImg Method to plot the genes according to their frequency in a microarray like image
URL: ../../../library/Rmagpie/html/rankedGenesImg-methods.html

Entry: runOneLayerExtCV-methods
Aliases: runOneLayerExtCV runOneLayerExtCV-methods runOneLayerExtCV,assessment-method
Keywords: methods
Description: runOneLayerExtCV: Method to run an external one-layer cross-validation
URL: ../../../library/Rmagpie/html/runOneLayerExtCV-methods.html

Entry: runTwoLayerExtCV-methods
Aliases: runTwoLayerExtCV-methods runTwoLayerExtCV runTwoLayerExtCV,assessment-method
Keywords: methods
Description: runTwoLayerExtCV: Method to run an external two-layers cross-validation
URL: ../../../library/Rmagpie/html/runTwoLayerExtCV-methods.html

Entry: setDataset-methods
Aliases: getDataset<- getDataset<--methods getDataset<-,assessment-method
Keywords: methods
Description: getDataset<- Method to modify the attributes of a dataset from an assessment
URL: ../../../library/Rmagpie/html/setDataset-methods.html

Entry: setFeatureSelectionOptions-methods
Aliases: getFeatureSelectionOptions<-,assessment-method getFeatureSelectionOptions<--methods getFeatureSelectionOptions<-
Keywords: methods
Description: getFeatureSelectionOptions<- Method to modify the attributes of a featureSelectionOptions from an assessment
URL: ../../../library/Rmagpie/html/setFeatureSelectionOptions-methods.html

Entry: show-methods
Aliases: show,assessment-method show,thresholds-method show,cvErrorRate-method show,cvErrorRate2ndLayer-method show,errorRate1stLayerCV-method show,errorRate2ndLayerCV-method show,finalClassifier-method show,frequencyGenes-method show,frequencyTopGenePerOneModel-method show,geneSubsets-method show,result2LayerCV-method show,resultRepeated1LayerCV-method show,resultRepeated2LayerCV-method show,resultSingle1LayerCV-method show,selectedGenes-method show,selectedGenes1stLayerCV-method show,selectedGenes2ndLayerCV-method show,selectedGenesPerOneOption-method
Keywords: methods
Description: show Display the object, by printing, plotting or whatever suits its class
URL: ../../../library/Rmagpie/html/show-methods.html

Entry: thresholds-class
Aliases: thresholds-class getNoThresholds,thresholds-method getNoThresholds<-,thresholds-method getNoThresholds getNoThresholds<- getOptionValues,thresholds-method getOptionValues<-,thresholds-method getOptionValues getOptionValues<-
Keywords: classes
Description: thresholds: A class to handle the thresholds to be tested during training of the Nearest Shrunken Centroid
URL: ../../../library/Rmagpie/html/thresholds-class.html

Entry: vV70genes
Aliases: vV70genes
Keywords: datasets
Description: vV70genes: van't Veer et al. 70 best genes in an object of class dataset.
URL: ../../../library/Rmagpie/html/vV70genes.html
