MicroArray Gene-expression-based Program In Error rate estimation

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Documentation for package ‘Rmagpie’ version 1.6.0

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A C F G I P R S T V

-- A --

assessment-class assessment: A central class to perform one and two layers of external

-- C --

classifyNewSamples classifyNewSamples Method to classify new samples for a given
classifyNewSamples-method classifyNewSamples Method to classify new samples for a given
classifyNewSamples-methods classifyNewSamples Method to classify new samples for a given

-- F --

featureSelectionOptions-class "featureSelectionOptions": A virtual class to store the options of a
finalClassifier-class finalClassifier: A class to store the final classifier corresponding to
findFinalClassifier findFinalClassifier Method to train and build the final classifier
findFinalClassifier-method findFinalClassifier Method to train and build the final classifier
findFinalClassifier-methods findFinalClassifier Method to train and build the final classifier

-- G --

geneSubsets-class geneSubsets: A class to handle the sizes of gene susbets to be tested
getClassifierName assessment: A central class to perform one and two layers of external
getClassifierName-method assessment: A central class to perform one and two layers of external
getClassifierName<- assessment: A central class to perform one and two layers of external
getClassifierName<--method assessment: A central class to perform one and two layers of external
getDataset getDataset Method to access the attributes of a dataset from an
getDataset-method getDataset Method to access the attributes of a dataset from an
getDataset-methods getDataset Method to access the attributes of a dataset from an
getDataset<- getDataset<- Method to modify the attributes of a dataset from an
getDataset<--method getDataset<- Method to modify the attributes of a dataset from an
getDataset<--methods getDataset<- Method to modify the attributes of a dataset from an
getFeatureSelectionMethod-method assessment: A central class to perform one and two layers of external
getFeatureSelectionOptions getFeatureSelectionOptions Method to access the attributes of a
getFeatureSelectionOptions-method getFeatureSelectionOptions Method to access the attributes of a
getFeatureSelectionOptions-methods getFeatureSelectionOptions Method to access the attributes of a
getFeatureSelectionOptions<- getFeatureSelectionOptions<- Method to modify the attributes of a
getFeatureSelectionOptions<--method getFeatureSelectionOptions<- Method to modify the attributes of a
getFeatureSelectionOptions<--methods getFeatureSelectionOptions<- Method to modify the attributes of a
getFinalClassifier getFinalClassifier Method to access the attributes of a finalClassifier
getFinalClassifier-method getFinalClassifier Method to access the attributes of a finalClassifier
getFinalClassifier-methods getFinalClassifier Method to access the attributes of a finalClassifier
getGenesFromBestToWorst finalClassifier: A class to store the final classifier corresponding to
getGenesFromBestToWorst-method finalClassifier: A class to store the final classifier corresponding to
getMaxSubsetSize geneSubsets: A class to handle the sizes of gene susbets to be tested
getMaxSubsetSize-method geneSubsets: A class to handle the sizes of gene susbets to be tested
getMaxSubsetSize<- geneSubsets: A class to handle the sizes of gene susbets to be tested
getMaxSubsetSize<--method geneSubsets: A class to handle the sizes of gene susbets to be tested
getModels finalClassifier: A class to store the final classifier corresponding to
getModels-method finalClassifier: A class to store the final classifier corresponding to
getNoFolds1stLayer assessment: A central class to perform one and two layers of external
getNoFolds1stLayer-method assessment: A central class to perform one and two layers of external
getNoFolds1stLayer<- assessment: A central class to perform one and two layers of external
getNoFolds1stLayer<--method assessment: A central class to perform one and two layers of external
getNoFolds2ndLayer assessment: A central class to perform one and two layers of external
getNoFolds2ndLayer-method assessment: A central class to perform one and two layers of external
getNoFolds2ndLayer<- assessment: A central class to perform one and two layers of external
getNoFolds2ndLayer<--method assessment: A central class to perform one and two layers of external
getNoModels geneSubsets: A class to handle the sizes of gene susbets to be tested
getNoModels-method geneSubsets: A class to handle the sizes of gene susbets to be tested
getNoOfRepeats assessment: A central class to perform one and two layers of external
getNoOfRepeats-method assessment: A central class to perform one and two layers of external
getNoOfRepeats<- assessment: A central class to perform one and two layers of external
getNoOfRepeats<--method assessment: A central class to perform one and two layers of external
getNoThresholds thresholds: A class to handle the thresholds to be tested during
getNoThresholds-method thresholds: A class to handle the thresholds to be tested during
getNoThresholds<- thresholds: A class to handle the thresholds to be tested during
getNoThresholds<--method thresholds: A class to handle the thresholds to be tested during
getOptionValues thresholds: A class to handle the thresholds to be tested during
getOptionValues-method "featureSelectionOptions": A virtual class to store the options of a
getOptionValues-method thresholds: A class to handle the thresholds to be tested during
getOptionValues<- thresholds: A class to handle the thresholds to be tested during
getOptionValues<--method thresholds: A class to handle the thresholds to be tested during
getResult1LayerCV assessment: A central class to perform one and two layers of external
getResult1LayerCV-method assessment: A central class to perform one and two layers of external
getResult1LayerCV<- assessment: A central class to perform one and two layers of external
getResult1LayerCV<--method assessment: A central class to perform one and two layers of external
getResult2LayerCV assessment: A central class to perform one and two layers of external
getResult2LayerCV-method assessment: A central class to perform one and two layers of external
getResult2LayerCV<- assessment: A central class to perform one and two layers of external
getResult2LayerCV<--method assessment: A central class to perform one and two layers of external
getResults getResults Method to access the result of one-layer and two-layers
getResults-method getResults Method to access the result of one-layer and two-layers
getResults-methods getResults Method to access the result of one-layer and two-layers
getSpeed geneSubsets: A class to handle the sizes of gene susbets to be tested
getSpeed-method geneSubsets: A class to handle the sizes of gene susbets to be tested
getSpeed<- geneSubsets: A class to handle the sizes of gene susbets to be tested
getSpeed<--method geneSubsets: A class to handle the sizes of gene susbets to be tested
getSubsetsSizes geneSubsets: A class to handle the sizes of gene susbets to be tested
getSubsetsSizes-method geneSubsets: A class to handle the sizes of gene susbets to be tested
getSubsetsSizes<- geneSubsets: A class to handle the sizes of gene susbets to be tested
getSubsetsSizes<--method geneSubsets: A class to handle the sizes of gene susbets to be tested
getSvmKernel assessment: A central class to perform one and two layers of external
getSvmKernel-method assessment: A central class to perform one and two layers of external
getSvmKernel<- assessment: A central class to perform one and two layers of external
getSvmKernel<--method assessment: A central class to perform one and two layers of external
getTypeFoldCreation assessment: A central class to perform one and two layers of external
getTypeFoldCreation-method assessment: A central class to perform one and two layers of external
getTypeFoldCreation<- assessment: A central class to perform one and two layers of external
getTypeFoldCreation<--method assessment: A central class to perform one and two layers of external

-- I --

initialize-method Initialize objects of class from Rmagpie

-- P --

plotErrorsFoldTwoLayerCV plotErrorsFoldTwoLayerCV Method to plot the error rate of a two-layer
plotErrorsFoldTwoLayerCV-method plotErrorsFoldTwoLayerCV Method to plot the error rate of a two-layer
plotErrorsFoldTwoLayerCV-methods plotErrorsFoldTwoLayerCV Method to plot the error rate of a two-layer
plotErrorsRepeatedOneLayerCV plotErrorsRepeatedOneLayerCV Method to plot the estimated error rates
plotErrorsRepeatedOneLayerCV-method plotErrorsRepeatedOneLayerCV Method to plot the estimated error rates
plotErrorsRepeatedOneLayerCV-methods plotErrorsRepeatedOneLayerCV Method to plot the estimated error rates
plotErrorsSummaryOneLayerCV plotErrorsSummaryOneLayerCV Method to plot the summary estimated error
plotErrorsSummaryOneLayerCV-method plotErrorsSummaryOneLayerCV Method to plot the summary estimated error
plotErrorsSummaryOneLayerCV-methods plotErrorsSummaryOneLayerCV Method to plot the summary estimated error

-- R --

rankedGenesImg rankedGenesImg Method to plot the genes according to their frequency in
rankedGenesImg-method rankedGenesImg Method to plot the genes according to their frequency in
rankedGenesImg-methods rankedGenesImg Method to plot the genes according to their frequency in
runOneLayerExtCV runOneLayerExtCV: Method to run an external one-layer cross-validation
runOneLayerExtCV-method runOneLayerExtCV: Method to run an external one-layer cross-validation
runOneLayerExtCV-methods runOneLayerExtCV: Method to run an external one-layer cross-validation
runTwoLayerExtCV runTwoLayerExtCV: Method to run an external two-layers cross-validation
runTwoLayerExtCV-method runTwoLayerExtCV: Method to run an external two-layers cross-validation
runTwoLayerExtCV-methods runTwoLayerExtCV: Method to run an external two-layers cross-validation

-- S --

show-method show Display the object, by printing, plotting or whatever suits its

-- T --

thresholds-class thresholds: A class to handle the thresholds to be tested during

-- V --

vV70genes vV70genes: van't Veer et al. 70 best genes in an object of class