Entry: CMA-package
Aliases: CMA-package CMA
Keywords: multivariate
Description: Synthesis of microarray-based classification
URL: ../../../library/CMA/html/CMA-package.html

Entry: ElasticNetCMA-methods
Aliases: ElasticNetCMA-methods ElasticNetCMA,matrix,numeric,missing-method ElasticNetCMA,matrix,factor,missing-method ElasticNetCMA,data.frame,missing,formula-method ElasticNetCMA,ExpressionSet,character,missing-method
Keywords: multivariate
Description: Classfication and variable selection by the ElasticNet
URL: ../../../library/CMA/html/ElasticNetCMA-methods.html

Entry: ElasticNetCMA
Aliases: ElasticNetCMA
Keywords: multivariate
Description: Classfication and variable selection by the ElasticNet
URL: ../../../library/CMA/html/ElasticNetCMA.html

Entry: GeneSelection-methods
Aliases: GeneSelection-methods GeneSelection,matrix,numeric,missing-method GeneSelection,matrix,factor,missing-method GeneSelection,data.frame,missing,formula-method GeneSelection,ExpressionSet,character,missing-method
Keywords: multivariate
Description: General method for variable selection with various methods
URL: ../../../library/CMA/html/GeneSelection-methods.html

Entry: GeneSelection
Aliases: GeneSelection
Keywords: multivariate
Description: General method for variable selection with various methods
URL: ../../../library/CMA/html/GeneSelection.html

Entry: GenerateLearningsets
Aliases: GenerateLearningsets
Keywords: multivariate
Description: Repeated Divisions into learn- and tets sets
URL: ../../../library/CMA/html/GenerateLearningsets.html

Entry: LassoCMA-methods
Aliases: LassoCMA-methods LassoCMA,matrix,numeric,missing-method LassoCMA,matrix,factor,missing-method LassoCMA,data.frame,missing,formula-method LassoCMA,ExpressionSet,character,missing-method
Keywords: multivariate
Description: L1 penalized logistic regression
URL: ../../../library/CMA/html/LassoCMA-methods.html

Entry: LassoCMA
Aliases: LassoCMA
Keywords: multivariate
Description: L1 penalized logistic regression
URL: ../../../library/CMA/html/LassoCMA.html

Entry: Planarplot-methods
Aliases: Planarplot-methods Planarplot,matrix,numeric,missing-method Planarplot,matrix,factor,missing-method Planarplot,data.frame,missing,formula-method Planarplot,ExpressionSet,character,missing-method
Keywords: multivariate
Description: Visualize Separability of different classes
URL: ../../../library/CMA/html/Planarplot-methods.html

Entry: Planarplot
Aliases: Planarplot
Keywords: multivariate
Description: Visualize Separability of different classes
URL: ../../../library/CMA/html/Planarplot.html

Entry: best
Aliases: best,tuningresult-method best
Keywords: multivariate
Description: Show best hyperparameter settings
URL: ../../../library/CMA/html/best.html

Entry: boxplot
Aliases: boxplot,evaloutput-method
Keywords: multivariate
Description: Make a boxplot of the classifier evaluation
URL: ../../../library/CMA/html/boxplot.html

Entry: classification-methods
Aliases: classification-methods classification,matrix,numeric,missing-method classification,matrix,factor,missing-method classification,data.frame,missing,formula-method classification,ExpressionSet,character,missing-method
Keywords: multivariate
Description: General method for classification with various methods
URL: ../../../library/CMA/html/classification-methods.html

Entry: classification
Aliases: classification
Keywords: multivariate
Description: General method for classification with various methods
URL: ../../../library/CMA/html/classification.html

Entry: cloutput-class
Aliases: cloutput-class cloutput show,cloutput-method
Keywords: multivariate
Description: "cloutput"
URL: ../../../library/CMA/html/cloutput-class.html

Entry: clvarseloutput-class
Aliases: clvarseloutput-class clvarseloutput
Keywords: multivariate
Description: "clvarseloutput"
URL: ../../../library/CMA/html/clvarseloutput-class.html

Entry: compBoostCMA-methods
Aliases: compBoostCMA-methods compBoostCMA,matrix,numeric,missing-method compBoostCMA,matrix,factor,missing-method compBoostCMA,data.frame,missing,formula-method compBoostCMA,ExpressionSet,character,missing-method
Keywords: multivariate
Description: Componentwise Boosting
URL: ../../../library/CMA/html/compBoostCMA-methods.html

Entry: compBoostCMA
Aliases: compBoostCMA
Keywords: multivariate
Description: Componentwise Boosting
URL: ../../../library/CMA/html/compBoostCMA.html

Entry: compare-methods
Aliases: compare-methods compare,list-method
Keywords: multivariate
Description: Compare different classifiers
URL: ../../../library/CMA/html/compare-methods.html

Entry: compare
Aliases: compare
Keywords: multivariate
Description: Compare different classifiers
URL: ../../../library/CMA/html/compare.html

Entry: dldaCMA-methods
Aliases: dldaCMA-methods dldaCMA,matrix,numeric,missing-method dldaCMA,matrix,factor,missing-method dldaCMA,data.frame,missing,formula-method dldaCMA,ExpressionSet,character,missing-method
Keywords: multivariate
Description: Diagonal Discriminant Analysis
URL: ../../../library/CMA/html/dldaCMA-methods.html

Entry: dldaCMA
Aliases: dldaCMA
Keywords: multivariate
Description: Diagonal Discriminant Analysis
URL: ../../../library/CMA/html/dldaCMA.html

Entry: evaloutput-class
Aliases: evaloutput-class evaloutput obsinfo,evaloutput-method show,evaloutput-method
Keywords: multivariate
Description: "evaloutput"
URL: ../../../library/CMA/html/evaloutput-class.html

Entry: evaluation-methods
Aliases: evaluation-methods evaluation,list-method
Keywords: multivariate
Description: Evaluation of classifiers
URL: ../../../library/CMA/html/evaluation-methods.html

Entry: evaluation
Aliases: evaluation
Keywords: multivariate
Description: Evaluation of classifiers
URL: ../../../library/CMA/html/evaluation.html

Entry: fdaCMA-methods
Aliases: fdaCMA-methods fdaCMA,matrix,numeric,missing-method fdaCMA,matrix,factor,missing-method fdaCMA,data.frame,missing,formula-method fdaCMA,ExpressionSet,character,missing-method
Keywords: multivariate
Description: Fisher's Linear Discriminant Analysis
URL: ../../../library/CMA/html/fdaCMA-methods.html

Entry: fdaCMA
Aliases: fdaCMA
Keywords: multivariate
Description: Fisher's Linear Discriminant Analysis
URL: ../../../library/CMA/html/fdaCMA.html

Entry: filter
Aliases: ttest welchtest wilcoxtest ftest kruskaltest limmatest golubcrit rfe
Keywords: multivariate
Description: Filter functions for Gene Selection
URL: ../../../library/CMA/html/filter.html

Entry: flexdaCMA-methods
Aliases: flexdaCMA-methods flexdaCMA,matrix,numeric,missing-method flexdaCMA,matrix,factor,missing-method flexdaCMA,data.frame,missing,formula-method flexdaCMA,ExpressionSet,character,missing-method
Keywords: multivariate
Description: Flexible Discriminant Analysis
URL: ../../../library/CMA/html/flexdaCMA-methods.html

Entry: flexdaCMA
Aliases: flexdaCMA
Keywords: multivariate
Description: Flexible Discriminant Analysis
URL: ../../../library/CMA/html/flexdaCMA.html

Entry: ftable
Aliases: ftable,cloutput-method
Keywords: multivariate
Description: Cross-tabulation of predicted and true class labels
URL: ../../../library/CMA/html/ftable.html

Entry: gbmCMA-methods
Aliases: gbmCMA-methods gbmCMA,matrix,numeric,missing-method gbmCMA,matrix,factor,missing-method gbmCMA,data.frame,missing,formula-method gbmCMA,ExpressionSet,character,missing-method
Keywords: multivariate
Description: Tree-based Gradient Boosting
URL: ../../../library/CMA/html/gbmCMA-methods.html

Entry: gbmCMA
Aliases: gbmCMA
Keywords: multivariate
Description: Tree-based Gradient Boosting
URL: ../../../library/CMA/html/gbmCMA.html

Entry: genesel-class
Aliases: genesel-class genesel show,genesel-method
Keywords: multivariate
Description: "genesel"
URL: ../../../library/CMA/html/genesel-class.html

Entry: golub
Aliases: golub
Keywords: datasets
Description: ALL/AML dataset of Golub et al. (1999)
URL: ../../../library/CMA/html/golub.html

Entry: internals
Aliases: plotprob roundvector rowswaps ROCinternal bklr bkreg bklr.predict care.exp care.dev mklr mkreg mklr.predict my.care.exp characterplot safeexp
Keywords: multivariate
Description: Internal functions
URL: ../../../library/CMA/html/internals.html

Entry: join-methods
Aliases: join-methods join,list-method
Keywords: multivariate
Description: Combine list elements returned by the method classification
URL: ../../../library/CMA/html/join-methods.html

Entry: join
Aliases: join
Keywords: multivariate
Description: Combine list elements returned by the method classification
URL: ../../../library/CMA/html/join.html

Entry: khan
Aliases: khan
Keywords: datasets
Description: Small blue round cell tumor dataset of Khan et al. (2001)
URL: ../../../library/CMA/html/khan.html

Entry: knnCMA-methods
Aliases: knnCMA-methods knnCMA,matrix,numeric,missing-method knnCMA,matrix,factor,missing-method knnCMA,data.frame,missing,formula-method knnCMA,ExpressionSet,character,missing-method
Keywords: multivariate
Description: Nearest Neighbours
URL: ../../../library/CMA/html/knnCMA-methods.html

Entry: knnCMA
Aliases: knnCMA
Keywords: multivariate
Description: Nearest Neighbours
URL: ../../../library/CMA/html/knnCMA.html

Entry: ldaCMA-methods
Aliases: ldaCMA-methods ldaCMA,matrix,numeric,missing-method ldaCMA,matrix,factor,missing-method ldaCMA,data.frame,missing,formula-method ldaCMA,ExpressionSet,character,missing-method
Keywords: multivariate
Description: Linear Discriminant Analysis
URL: ../../../library/CMA/html/ldaCMA-methods.html

Entry: ldaCMA
Aliases: ldaCMA
Keywords: multivariate
Description: Linear Discriminant Analysis
URL: ../../../library/CMA/html/ldaCMA.html

Entry: learningsets-class
Aliases: learningsets-class learningsets show,learningsets-method
Keywords: multivariate
Description: "learningsets"
URL: ../../../library/CMA/html/learningsets-class.html

Entry: nnetCMA-methods
Aliases: nnetCMA-methods nnetCMA,matrix,numeric,missing-method nnetCMA,matrix,factor,missing-method nnetCMA,data.frame,missing,formula-method nnetCMA,ExpressionSet,character,missing-method
Keywords: multivariate
Description: Feed-Forward Neural Networks
URL: ../../../library/CMA/html/nnetCMA-methods.html

Entry: nnetCMA
Aliases: nnetCMA
Keywords: multivariate
Description: Feed-forward Neural Networks
URL: ../../../library/CMA/html/nnetCMA.html

Entry: obsinfo
Aliases: obsinfo
Keywords: multivariate
Description: Classifiability of observations
URL: ../../../library/CMA/html/obsinfo.html

Entry: pknnCMA-methods
Aliases: pknnCMA-methods pknnCMA,matrix,numeric,missing-method pknnCMA,matrix,factor,missing-method pknnCMA,data.frame,missing,formula-method pknnCMA,ExpressionSet,character,missing-method
Keywords: multivariate
Description: Probabilistic nearest neighbours
URL: ../../../library/CMA/html/pknnCMA-methods.html

Entry: pknnCMA
Aliases: pknnCMA
Keywords: multivariate
Description: Probabilistic Nearest Neighbours
URL: ../../../library/CMA/html/pknnCMA.html

Entry: plot
Aliases: plot,cloutput-method plot,cloutput-method plot,cloutput,missing-method
Keywords: multivariate
Description: Probability plot
URL: ../../../library/CMA/html/plot,cloutput-method.html

Entry: Barplot
Aliases: plot,genesel-method plot,genesel,missing-method
Keywords: multivariate
Description: Barplot of variable importance
URL: ../../../library/CMA/html/plot,genesel-method.html

Entry: plot tuningresult
Aliases: plot,tuningresult-method plot,tuningresult,missing-method
Keywords: multivariate
Description: Visualize results of tuning
URL: ../../../library/CMA/html/plot,tuningresult-method.html

Entry: plrCMA-methods
Aliases: plrCMA-methods plrCMA,matrix,numeric,missing-method plrCMA,matrix,factor,missing-method plrCMA,data.frame,missing,formula-method plrCMA,ExpressionSet,character,missing-method
Keywords: multivariate
Description: L2 penalized logistic regression
URL: ../../../library/CMA/html/plrCMA-methods.html

Entry: plrCMA
Aliases: plrCMA
Keywords: multivariate
Description: L2 penalized logistic regression
URL: ../../../library/CMA/html/plrCMA.html

Entry: pls_ldaCMA-methods
Aliases: pls_ldaCMA-methods pls_ldaCMA,matrix,numeric,missing-method pls_ldaCMA,matrix,factor,missing-method pls_ldaCMA,data.frame,missing,formula-method pls_ldaCMA,ExpressionSet,character,missing-method
Keywords: multivariate
Description: Partial Least Squares combined with Linear Discriminant Analysis
URL: ../../../library/CMA/html/pls_ldaCMA-methods.html

Entry: pls_ldaCMA
Aliases: pls_ldaCMA
Keywords: multivariate
Description: Partial Least Squares combined with Linear Discriminant Analysis
URL: ../../../library/CMA/html/pls_ldaCMA.html

Entry: pls_lrCMA-methods
Aliases: pls_lrCMA-methods pls_lrCMA,matrix,numeric,missing-method pls_lrCMA,matrix,factor,missing-method pls_lrCMA,data.frame,missing,formula-method pls_lrCMA,ExpressionSet,character,missing-method
Keywords: multivariate
Description: Partial Least Squares followed by logistic regression
URL: ../../../library/CMA/html/pls_lrCMA-methods.html

Entry: pls_lrCMA
Aliases: pls_lrCMA
Keywords: multivariate
Description: Partial Least Squares followed by logistic regression
URL: ../../../library/CMA/html/pls_lrCMA.html

Entry: pls_rfCMA-methods
Aliases: pls_rfCMA-methods pls_rfCMA,matrix,numeric,missing-method pls_rfCMA,matrix,factor,missing-method pls_rfCMA,data.frame,missing,formula-method pls_rfCMA,ExpressionSet,character,missing-method
Keywords: multivariate
Description: Partial Least Squares followed by random forests
URL: ../../../library/CMA/html/pls_rfCMA-methods.html

Entry: pls_rfCMA
Aliases: pls_rfCMA
Keywords: multivariate
Description: Partial Least Squares followed by random forests
URL: ../../../library/CMA/html/pls_rfCMA.html

Entry: pnnCMA-methods
Aliases: pnnCMA-methods pnnCMA,matrix,numeric,missing-method pnnCMA,matrix,factor,missing-method pnnCMA,data.frame,missing,formula-method pnnCMA,ExpressionSet,character,missing-method
Keywords: multivariate
Description: Probabilistic Neural Networks
URL: ../../../library/CMA/html/pnnCMA-methods.html

Entry: pnnCMA
Aliases: pnnCMA
Keywords: multivariate
Description: Probabilistic Neural Networks
URL: ../../../library/CMA/html/pnnCMA.html

Entry: prediction-methods
Aliases: prediction-methods prediction,matrix,ANY,matrix,missing-method prediction,data.frame,missing,data.frame,formula-method prediction,ExpressionSet,character,ExpressionSet,missing-method
Keywords: multivariate
Description: General method for predicting class lables of new observations
URL: ../../../library/CMA/html/prediction-methods.html

Entry: prediction
Aliases: prediction
Keywords: multivariate
Description: General method for predicting classes of new observations
URL: ../../../library/CMA/html/prediction.html

Entry: predoutput-class
Aliases: predoutput-class predoutput show,predoutput-method
Keywords: multivariate
Description: "predoutput"
URL: ../../../library/CMA/html/predoutput-class.html

Entry: qdaCMA-methods
Aliases: qdaCMA-methods qdaCMA,matrix,numeric,missing-method qdaCMA,matrix,factor,missing-method qdaCMA,data.frame,missing,formula-method qdaCMA,ExpressionSet,character,missing-method
Keywords: multivariate
Description: Quadratic Discriminant Analysis
URL: ../../../library/CMA/html/qdaCMA-methods.html

Entry: qdaCMA
Aliases: qdaCMA
Keywords: multivariate
Description: Quadratic Discriminant Analysis
URL: ../../../library/CMA/html/qdaCMA.html

Entry: rfCMA-methods
Aliases: rfCMA-methods rfCMA,matrix,numeric,missing-method rfCMA,matrix,factor,missing-method rfCMA,data.frame,missing,formula-method rfCMA,ExpressionSet,character,missing-method
Keywords: multivariate
Description: Classification based on Random Forests
URL: ../../../library/CMA/html/rfCMA-methods.html

Entry: rfCMA
Aliases: rfCMA
Keywords: multivariate
Description: Classification based on Random Forests
URL: ../../../library/CMA/html/rfCMA.html

Entry: roc
Aliases: roc,cloutput-method roc
Keywords: multivariate
Description: Receiver Operator Characteristic
URL: ../../../library/CMA/html/roc.html

Entry: scdaCMA-methods
Aliases: scdaCMA-methods scdaCMA,matrix,numeric,missing-method scdaCMA,matrix,factor,missing-method scdaCMA,data.frame,missing,formula-method scdaCMA,ExpressionSet,character,missing-method
Keywords: multivariate
Description: Shrunken Centroids Discriminant Analysis
URL: ../../../library/CMA/html/scdaCMA-methods.html

Entry: scdaCMA
Aliases: scdaCMA
Keywords: multivariate
Description: Shrunken Centroids Discriminant Analysis
URL: ../../../library/CMA/html/scdaCMA.html

Entry: shrinkldaCMA-methods
Aliases: shrinkldaCMA-methods shrinkldaCMA,matrix,numeric,missing-method shrinkldaCMA,matrix,factor,missing-method shrinkldaCMA,data.frame,missing,formula-method shrinkldaCMA,ExpressionSet,character,missing-method
Keywords: multivariate
Description: Shrinkage linear discriminant analysis
URL: ../../../library/CMA/html/shrinkldaCMA-methods.html

Entry: shrinkldaCMA
Aliases: shrinkldaCMA
Keywords: multivariate
Description: Shrinkage linear discriminant analysis
URL: ../../../library/CMA/html/shrinkldaCMA.html

Entry: summary
Aliases: summary,evaloutput-method
Keywords: multivariate
Description: Summarize classifier evaluation
URL: ../../../library/CMA/html/summary.html

Entry: svmCMA-methods
Aliases: svmCMA-methods svmCMA,matrix,numeric,missing-method svmCMA,matrix,factor,missing-method svmCMA,data.frame,missing,formula-method svmCMA,ExpressionSet,character,missing-method
Keywords: multivariate
Description: Support Vector Machine
URL: ../../../library/CMA/html/svmCMA-methods.html

Entry: svmCMA
Aliases: svmCMA
Keywords: multivariate
Description: Support Vector Machine
URL: ../../../library/CMA/html/svmCMA.html

Entry: toplist
Aliases: toplist toplist,genesel-method
Keywords: multivariate
Description: Display 'top' variables
URL: ../../../library/CMA/html/toplist.html

Entry: tune-methods
Aliases: tune-methods tune,matrix,numeric,missing-method tune,matrix,factor,missing-method tune,data.frame,missing,formula-method tune,ExpressionSet,character,missing-method
Keywords: multivariate
Description: Hyperparameter tuning for classifiers
URL: ../../../library/CMA/html/tune-methods.html

Entry: tune
Aliases: tune
Keywords: multivariate
Description: Hyperparameter tuning for classifiers
URL: ../../../library/CMA/html/tune.html

Entry: tuningresult-class
Aliases: tuningresult-class tuningresult show,tuningresult-method
Keywords: multivariate
Description: "tuningresult"
URL: ../../../library/CMA/html/tuningresult-class.html

Entry: varseloutput-class
Aliases: varseloutput-class varseloutput
Keywords: multivariate
Description: "varseloutput"
URL: ../../../library/CMA/html/varseloutput-class.html
