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

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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.

Author
Camille Maumet <Rmagpie@gmail.com>, with contributions from C. Ambroise J. Zhu
Date of publication
None
Maintainer
Camille Maumet <Rmagpie@gmail.com>
License
GPL (>= 3)
Version
1.30.0
URLs

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...

Files in this package

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