Rmagpie: MicroArray Gene-expression-based Program In Error rate estimation
Version 1.32.0

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.

Browse man pages Browse package API and functions Browse package files

AuthorCamille Maumet <Rmagpie@gmail.com>, with contributions from C. Ambroise J. Zhu
Bioconductor views Classification Microarray
Date of publicationNone
MaintainerCamille Maumet <Rmagpie@gmail.com>
LicenseGPL (>= 3)
Version1.32.0
URL http://www.bioconductor.org/
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("Rmagpie")

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...
plotErrorsRepeatedOneLayerCV: plotErrorsRepeatedOneLayerCV Method to plot the estimated...
plotErrorsSummaryOneLayerCV-methods: plotErrorsSummaryOneLayerCV Method to plot the summary...
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

NSCFeatureSelection Source code
NSCTrainTest Source code
RFESVMFeatureSelection Source code
SVMTrainTest Source code
assessment-class Man page
classifyNewSamples Man page
classifyNewSamples,assessment-method Man page
classifyNewSamples-methods Man page
crossval.errors Source code
divideInFolds Source code
divideNaiveTestFolds Source code
divideNaiveTrainFolds Source code
divideTestFolds Source code
divideTrainFolds Source code
featureSelectionOptions-class Man page
finalClassifier-class Man page
findDJ Source code
findFinalClassifier Man page
findFinalClassifier,assessment-method Man page
findFinalClassifier-methods Man page
findPositionArrow Source code
findPositionsLegend Source code
findPositionsLegendWithFold Source code
frequencyTopGenes Source code
geneSubsets-class Man page
getAlpha Source code
getClassifierName Man page
getClassifierName,assessment-method Man page
getClassifierName<- Man page
getClassifierName<-,assessment-method Man page
getDataset Man page
getDataset,assessment-method Man page
getDataset-methods Man page
getDataset<- Man page
getDataset<-,assessment-method Man page
getDataset<--methods Man page
getFeatureSelectionMethod,assessment-method Man page
getFeatureSelectionOptions Man page
getFeatureSelectionOptions,assessment-method Man page
getFeatureSelectionOptions-methods Man page
getFeatureSelectionOptions<- Man page
getFeatureSelectionOptions<-,assessment-method 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,geneSubsets-method Man page
getMaxSubsetSize<- Man page
getMaxSubsetSize<-,geneSubsets-method Man page
getModels Man page
getModels,finalClassifier-method Man page
getNoFolds1stLayer Man page
getNoFolds1stLayer,assessment-method Man page
getNoFolds1stLayer<- Man page
getNoFolds1stLayer<-,assessment-method Man page
getNoFolds2ndLayer Man page
getNoFolds2ndLayer,assessment-method Man page
getNoFolds2ndLayer<- Man page
getNoFolds2ndLayer<-,assessment-method Man page
getNoModels Man page
getNoModels,geneSubsets-method Man page
getNoOfRepeats Man page
getNoOfRepeats,assessment-method Man page
getNoOfRepeats<- Man page
getNoOfRepeats<-,assessment-method Man page
getNoThresholds Man page
getNoThresholds,thresholds-method Man page
getNoThresholds<- Man page
getNoThresholds<-,thresholds-method Man page
getOptionValues Man page
getOptionValues,featureSelectionOptions-method Man page
getOptionValues,thresholds-method Man page
getOptionValues<- Man page
getOptionValues<-,thresholds-method Man page
getResult1LayerCV Man page
getResult1LayerCV,assessment-method Man page
getResult1LayerCV<- Man page
getResult1LayerCV<-,assessment-method Man page
getResult2LayerCV Man page
getResult2LayerCV,assessment-method Man page
getResult2LayerCV<- Man page
getResult2LayerCV<-,assessment-method Man page
getResults Man page
getResults,assessment-method Man page
getResults-methods Man page
getSpeed Man page
getSpeed,geneSubsets-method Man page
getSpeed<- Man page
getSpeed<-,geneSubsets-method Man page
getSubsetsSizes Man page
getSubsetsSizes,geneSubsets-method Man page
getSubsetsSizes<- Man page
getSubsetsSizes<-,geneSubsets-method Man page
getSvmKernel Man page
getSvmKernel,assessment-method Man page
getSvmKernel<- Man page
getSvmKernel<-,assessment-method Man page
getTypeFoldCreation Man page
getTypeFoldCreation,assessment-method Man page
getTypeFoldCreation<- Man page
getTypeFoldCreation<-,assessment-method Man page
getW Source code
getY Source code
imageGene Source code
initialize,assessment-method Man page
initialize,geneSubsets-method Man page
initialize,thresholds-method Man page
linear.feasel Source code
loadData Source code
noFvec Source code
oneLayerExtCV Source code
orderFeatures Source code
performACvPerModelWithNSCAndNSC Source code
performACvPerModelWithSVMAndRFE Source code
performAValidation Source code
plotErrorRatePerFold Source code
plotErrors Source code
plotErrorsFoldTwoLayerCV Man page
plotErrorsFoldTwoLayerCV,assessment-method Man page
plotErrorsFoldTwoLayerCV-methods Man page
plotErrorsRepeatedOneLayerCV Man page
plotErrorsRepeatedOneLayerCV,assessment-method Man page
plotErrorsRepeatedOneLayerCV-methods Man page
plotErrorsSummaryOneLayerCV Man page
plotErrorsSummaryOneLayerCV,assessment-method Man page
plotErrorsSummaryOneLayerCV-methods Man page
printImageGenes Source code
rankedGenesImg Man page
rankedGenesImg,assessment-method Man page
rankedGenesImg-methods Man page
rfe.cv Source code
rfe.fit Source code
rfe.predict Source code
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,cvErrorRate-method Man page
show,cvErrorRate2ndLayer-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,selectedGenes-method Man page
show,selectedGenes1stLayerCV-method Man page
show,selectedGenes2ndLayerCV-method Man page
show,selectedGenesPerOneOption-method Man page
show,thresholds-method Man page
superpose.eb Source code
svm.weight Source code
test.nonDim0NumericMatrix Source code
test.nonLength0 Source code
test.nonLength0Vector Source code
test.oneElement Source code
thresholds-class Man page
twoLayerExtCV Source code
vV70genes Man page

Files

DESCRIPTION
LICENSE.txt
NAMESPACE
R
R/AllClasses.R
R/AllGenerics.R
R/classifyNewSamples.R
R/experiment-accessors.R
R/featureSelectionOptions-accessors.R
R/finalClassifier-accessors.R
R/geneSubsets-accessors.R
R/initialize-methods.R
R/loadData-methods.R
R/non_linear_svm.R
R/one_layer_ext_CV.R
R/rateGenes.R
R/result2LayerCV-accessors.R
R/resultRepeated1LayerCV-accessors.R
R/rfe.R
R/runOneLayerExtCV-methods.R
R/runTwoLayerExtCV-methods.R
R/setValidity-methods.R
R/show-methods.R
R/thresholds-accessors.R
R/tool_case.R
R/two_layer_ext_CV.R
R/typeValidity.R
R/user_interface.R
build
build/vignette.rds
data
data/vV70genesDataset.rda
demo
demo/00Index
demo/demoCV.R
demo/demoClassifyNewSample.R
demo/demoPlots.r
inst
inst/doc
inst/doc/Magpie_examples.R
inst/doc/Magpie_examples.Rnw
inst/doc/Magpie_examples.pdf
inst/extdata
inst/extdata/raw_classes.txt
inst/extdata/raw_geneExpr.txt
inst/extdata/vV_newSamples.txt
man
man/classifyNewSamples-methods.Rd
man/experiment-class.Rd
man/featureSelectionOptions-class.Rd
man/finalClassifier-class.Rd
man/findFinalClassifier-methods.Rd
man/geneSubsets-class.Rd
man/getDataset-methods.Rd
man/getFeatureSelectionOptions-methods.Rd
man/getFinalClassifier.Rd
man/getResults-methods.Rd
man/initialize-methods.Rd
man/plotErrorsFoldTwoLayerCV-methods.Rd
man/plotErrorsRepeatedOneLayerCV.rd
man/plotErrorsSummaryOneLayerCV-methods.rd
man/rankedGenesImg-methods.Rd
man/runOneLayerExtCV-methods.Rd
man/runTwoLayerExtCV-methods.Rd
man/setDataset-methods.Rd
man/setFeatureSelectionOptions-methods.Rd
man/show-methods.Rd
man/thresholds-class.Rd
man/vV70genes.Rd
vignettes
vignettes/Magpie_examples.Rnw
vignettes/literature.bib
Rmagpie documentation built on May 20, 2017, 10:41 p.m.