Rmagpie: MicroArray Gene-expression-based Program In Error rate estimation

Microarray Classification is designed for both biologists and statisticians. It offers the ability to train a classifier on a labelled microarray dataset and to then use that classifier to predict the class of new observations. A range of modern classifiers are available, including support vector machines (SVMs), nearest shrunken centroids (NSCs)... Advanced methods are provided to estimate the predictive error rate and to report the subset of genes which appear essential in discriminating between classes.

AuthorCamille Maumet <Rmagpie@gmail.com>, with contributions from C. Ambroise J. Zhu
Date of publicationNone
MaintainerCamille Maumet <Rmagpie@gmail.com>
LicenseGPL (>= 3)
Version1.30.0
http://www.bioconductor.org/

View on Bioconductor

Man pages

classifyNewSamples-methods: classifyNewSamples Method to classify new samples for a given...

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

featureSelectionOptions-class: "featureSelectionOptions": A virtual class to store the...

finalClassifier-class: finalClassifier: A class to store the final classifier...

findFinalClassifier-methods: findFinalClassifier Method to train and build the final...

geneSubsets-class: geneSubsets: A class to handle the sizes of gene susbets to...

getDataset-methods: getDataset Method to access the attributes of a dataset from...

getFeatureSelectionOptions-methods: getFeatureSelectionOptions Method to access the attributes of...

getFinalClassifier: getFinalClassifier Method to access the attributes of a...

getResults-methods: getResults Method to access the result of one-layer and...

initialize-methods: Initialize objects of class from Rmagpie

plotErrorsFoldTwoLayerCV-methods: plotErrorsFoldTwoLayerCV Method to plot the error rate of a...

rankedGenesImg-methods: rankedGenesImg Method to plot the genes according to their...

runOneLayerExtCV-methods: runOneLayerExtCV: Method to run an external one-layer...

runTwoLayerExtCV-methods: runTwoLayerExtCV: Method to run an external two-layers...

setDataset-methods: getDataset<- Method to modify the attributes of a dataset...

setFeatureSelectionOptions-methods: getFeatureSelectionOptions<- Method to modify the attributes...

show-methods: show Display the object, by printing, plotting or whatever...

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

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

Functions

assessment-class Man page
classifyNewSamples Man page
classifyNewSamples,assessment-method Man page
classifyNewSamples-methods Man page
featureSelectionOptions-class Man page
finalClassifier-class Man page
findFinalClassifier Man page
findFinalClassifier,assessment-method Man page
findFinalClassifier-methods Man page
geneSubsets-class Man page
getClassifierName Man page
getClassifierName<- Man page
getClassifierName<-,assessment-method Man page
getClassifierName,assessment-method Man page
getDataset Man page
getDataset<- Man page
getDataset<-,assessment-method Man page
getDataset,assessment-method Man page
getDataset<--methods Man page
getDataset-methods Man page
getFeatureSelectionMethod,assessment-method Man page
getFeatureSelectionOptions Man page
getFeatureSelectionOptions<- Man page
getFeatureSelectionOptions<-,assessment-method Man page
getFeatureSelectionOptions,assessment-method Man page
getFeatureSelectionOptions<--methods Man page
getFeatureSelectionOptions-methods Man page
getFinalClassifier Man page
getFinalClassifier,assessment-method Man page
getFinalClassifier-methods Man page
getGenesFromBestToWorst Man page
getGenesFromBestToWorst,finalClassifier-method Man page
getMaxSubsetSize Man page
getMaxSubsetSize<- Man page
getMaxSubsetSize<-,geneSubsets-method Man page
getMaxSubsetSize,geneSubsets-method Man page
getModels Man page
getModels,finalClassifier-method Man page
getNoFolds1stLayer Man page
getNoFolds1stLayer<- Man page
getNoFolds1stLayer<-,assessment-method Man page
getNoFolds1stLayer,assessment-method Man page
getNoFolds2ndLayer Man page
getNoFolds2ndLayer<- Man page
getNoFolds2ndLayer<-,assessment-method Man page
getNoFolds2ndLayer,assessment-method Man page
getNoModels Man page
getNoModels,geneSubsets-method Man page
getNoOfRepeats Man page
getNoOfRepeats<- Man page
getNoOfRepeats<-,assessment-method Man page
getNoOfRepeats,assessment-method Man page
getNoThresholds Man page
getNoThresholds<- Man page
getNoThresholds<-,thresholds-method Man page
getNoThresholds,thresholds-method Man page
getOptionValues Man page
getOptionValues<- Man page
getOptionValues,featureSelectionOptions-method Man page
getOptionValues<-,thresholds-method Man page
getOptionValues,thresholds-method Man page
getResult1LayerCV Man page
getResult1LayerCV<- Man page
getResult1LayerCV<-,assessment-method Man page
getResult1LayerCV,assessment-method Man page
getResult2LayerCV Man page
getResult2LayerCV<- Man page
getResult2LayerCV<-,assessment-method Man page
getResult2LayerCV,assessment-method Man page
getResults Man page
getResults,assessment-method Man page
getResults-methods Man page
getSpeed Man page
getSpeed<- Man page
getSpeed<-,geneSubsets-method Man page
getSpeed,geneSubsets-method Man page
getSubsetsSizes Man page
getSubsetsSizes<- Man page
getSubsetsSizes<-,geneSubsets-method Man page
getSubsetsSizes,geneSubsets-method Man page
getSvmKernel Man page
getSvmKernel<- Man page
getSvmKernel<-,assessment-method Man page
getSvmKernel,assessment-method Man page
getTypeFoldCreation Man page
getTypeFoldCreation<- Man page
getTypeFoldCreation<-,assessment-method Man page
getTypeFoldCreation,assessment-method Man page
initialize,assessment-method Man page
initialize,geneSubsets-method Man page
initialize,thresholds-method Man page
plotErrorsFoldTwoLayerCV Man page
plotErrorsFoldTwoLayerCV,assessment-method Man page
plotErrorsFoldTwoLayerCV-methods Man page
rankedGenesImg Man page
rankedGenesImg,assessment-method Man page
rankedGenesImg-methods Man page
runOneLayerExtCV Man page
runOneLayerExtCV,assessment-method Man page
runOneLayerExtCV-methods Man page
runTwoLayerExtCV Man page
runTwoLayerExtCV,assessment-method Man page
runTwoLayerExtCV-methods Man page
show,assessment-method Man page
show,cvErrorRate2ndLayer-method Man page
show,cvErrorRate-method Man page
show,errorRate1stLayerCV-method Man page
show,errorRate2ndLayerCV-method Man page
show,finalClassifier-method Man page
show,frequencyGenes-method Man page
show,frequencyTopGenePerOneModel-method Man page
show,geneSubsets-method Man page
show,result2LayerCV-method Man page
show,resultRepeated1LayerCV-method Man page
show,resultRepeated2LayerCV-method Man page
show,resultSingle1LayerCV-method Man page
show,selectedGenes1stLayerCV-method Man page
show,selectedGenes2ndLayerCV-method Man page
show,selectedGenes-method Man page
show,selectedGenesPerOneOption-method Man page
show,thresholds-method Man page
thresholds-class Man page
vV70genes Man page

Files

Rmagpie/DESCRIPTION
Rmagpie/LICENSE.txt
Rmagpie/NAMESPACE
Rmagpie/R
Rmagpie/R/AllClasses.R Rmagpie/R/AllGenerics.R Rmagpie/R/classifyNewSamples.R Rmagpie/R/experiment-accessors.R Rmagpie/R/featureSelectionOptions-accessors.R Rmagpie/R/finalClassifier-accessors.R Rmagpie/R/geneSubsets-accessors.R Rmagpie/R/initialize-methods.R Rmagpie/R/loadData-methods.R Rmagpie/R/non_linear_svm.R Rmagpie/R/one_layer_ext_CV.R Rmagpie/R/rateGenes.R Rmagpie/R/result2LayerCV-accessors.R Rmagpie/R/resultRepeated1LayerCV-accessors.R Rmagpie/R/rfe.R Rmagpie/R/runOneLayerExtCV-methods.R Rmagpie/R/runTwoLayerExtCV-methods.R Rmagpie/R/setValidity-methods.R Rmagpie/R/show-methods.R Rmagpie/R/thresholds-accessors.R Rmagpie/R/tool_case.R Rmagpie/R/two_layer_ext_CV.R Rmagpie/R/typeValidity.R Rmagpie/R/user_interface.R
Rmagpie/build
Rmagpie/build/vignette.rds
Rmagpie/data
Rmagpie/data/vV70genesDataset.rda
Rmagpie/demo
Rmagpie/demo/00Index
Rmagpie/demo/demoCV.R
Rmagpie/demo/demoClassifyNewSample.R
Rmagpie/demo/demoPlots.r
Rmagpie/inst
Rmagpie/inst/doc
Rmagpie/inst/doc/Magpie_examples.R
Rmagpie/inst/doc/Magpie_examples.Rnw
Rmagpie/inst/doc/Magpie_examples.pdf
Rmagpie/inst/extdata
Rmagpie/inst/extdata/raw_classes.txt
Rmagpie/inst/extdata/raw_geneExpr.txt
Rmagpie/inst/extdata/vV_newSamples.txt
Rmagpie/man
Rmagpie/man/classifyNewSamples-methods.Rd Rmagpie/man/experiment-class.Rd Rmagpie/man/featureSelectionOptions-class.Rd Rmagpie/man/finalClassifier-class.Rd Rmagpie/man/findFinalClassifier-methods.Rd Rmagpie/man/geneSubsets-class.Rd Rmagpie/man/getDataset-methods.Rd Rmagpie/man/getFeatureSelectionOptions-methods.Rd Rmagpie/man/getFinalClassifier.Rd Rmagpie/man/getResults-methods.Rd Rmagpie/man/initialize-methods.Rd Rmagpie/man/plotErrorsFoldTwoLayerCV-methods.Rd
Rmagpie/man/plotErrorsRepeatedOneLayerCV.rd
Rmagpie/man/plotErrorsSummaryOneLayerCV-methods.rd
Rmagpie/man/rankedGenesImg-methods.Rd Rmagpie/man/runOneLayerExtCV-methods.Rd Rmagpie/man/runTwoLayerExtCV-methods.Rd Rmagpie/man/setDataset-methods.Rd Rmagpie/man/setFeatureSelectionOptions-methods.Rd Rmagpie/man/show-methods.Rd Rmagpie/man/thresholds-class.Rd Rmagpie/man/vV70genes.Rd
Rmagpie/vignettes
Rmagpie/vignettes/Magpie_examples.Rnw
Rmagpie/vignettes/literature.bib

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