Package: CMA 1.71.0

Roman Hornung

CMA: Synthesis of microarray-based classification

This package provides a comprehensive collection of various microarray-based classification algorithms both from Machine Learning and Statistics. Variable Selection, Hyperparameter tuning, Evaluation and Comparison can be performed combined or stepwise in a user-friendly environment.

Authors:Martin Slawski <[email protected]>, Anne-Laure Boulesteix <[email protected]>, Christoph Bernau <[email protected]>.

CMA_1.71.0.tar.gz
CMA_1.71.0.zip(r-4.7)CMA_1.71.0.zip(r-4.6)CMA_1.71.0.zip(r-4.5)
CMA_1.71.0.tgz(r-4.6-any)CMA_1.71.0.tgz(r-4.5-any)
CMA_1.71.0.tar.gz(r-4.7-any)CMA_1.71.0.tar.gz(r-4.6-any)
CMA_1.71.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
CMA/json (API)

# Install 'CMA' in R:

install.packages('CMA', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

golub - ALL/AML dataset of Golub et al.
khan - Small blue round cell tumor dataset of Khan et al.

On BioConductor:CMA-1.71.0(bioc 3.24)CMA-1.70.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

classification decisiontree

5.18 score 76 scripts 337 mentions 49 exports 3 dependencies

Last updated from:b83e472a68. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	161
linux-devel-x86_64	NOTE	172
source / vignettes	OK	193
linux-release-x86_64	NOTE	168
macos-release-arm64	NOTE	89
macos-oldrel-arm64	NOTE	88
windows-devel	NOTE	105
windows-release	NOTE	103
windows-oldrel	NOTE	106
wasm-release	OK	123

Exports:best boxplot classification compare compBoostCMA dldaCMA ElasticNetCMA evaluation fdaCMA flexdaCMA ftable ftest gbmCMA GenerateLearningsets GeneSelection golubcrit join knnCMA kruskaltest LassoCMA ldaCMA limmatest nnetCMA obsinfo pknnCMA Planarplot plot plrCMA pls_ldaCMA pls_lrCMA pls_rfCMA pnnCMA prediction qdaCMA rfCMA rfe roc scdaCMA show shrinkldaCMA summary svmCMA toplist ttest tune weighted.mcr welchtest wilcoxtest wmc

Dependencies:Biobase BiocGenerics generics

CMA Manual

Rendered fromCMA_vignette.rnwusingutils::Sweave

Last update: 2013-11-01
Started: 2013-11-01

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Synthesis of microarray-based classification	CMA-package CMA
Barplot of variable importance	plot,genesel,missing-method plot,genesel-method
Show best hyperparameter settings	best best,tuningresult-method
Make a boxplot of the classifier evaluation	boxplot,evaloutput-method
General method for classification with various methods	classification
General method for classification with various methods	classification,data.frame,missing,formula-method classification,ExpressionSet,character,missing-method classification,matrix,factor,missing-method classification,matrix,numeric,missing-method classification-methods
"cloutput"	cloutput cloutput-class show,cloutput-method
"clvarseloutput"	clvarseloutput clvarseloutput-class
Compare different classifiers	compare
Compare different classifiers	compare,list-method compare-methods
Componentwise Boosting	compBoostCMA
Componentwise Boosting	compBoostCMA,data.frame,missing,formula-method compBoostCMA,ExpressionSet,character,missing-method compBoostCMA,matrix,factor,missing-method compBoostCMA,matrix,numeric,missing-method compBoostCMA-methods
Diagonal Discriminant Analysis	dldaCMA
Diagonal Discriminant Analysis	dldaCMA,data.frame,missing,formula-method dldaCMA,ExpressionSet,character,missing-method dldaCMA,matrix,factor,missing-method dldaCMA,matrix,numeric,missing-method dldaCMA-methods
Classfication and variable selection by the ElasticNet	ElasticNetCMA
Classfication and variable selection by the ElasticNet	ElasticNetCMA,data.frame,missing,formula-method ElasticNetCMA,ExpressionSet,character,missing-method ElasticNetCMA,matrix,factor,missing-method ElasticNetCMA,matrix,numeric,missing-method ElasticNetCMA-methods
"evaloutput"	evaloutput evaloutput-class obsinfo,evaloutput-method show,evaloutput-method
Evaluation of classifiers	evaluation
Evaluation of classifiers	evaluation,list-method evaluation-methods
Fisher's Linear Discriminant Analysis	fdaCMA
Fisher's Linear Discriminant Analysis	fdaCMA,data.frame,missing,formula-method fdaCMA,ExpressionSet,character,missing-method fdaCMA,matrix,factor,missing-method fdaCMA,matrix,numeric,missing-method fdaCMA-methods
Filter functions for Gene Selection	ftest golubcrit kruskaltest limmatest rfe shrinkcat ttest welchtest wilcoxtest
Flexible Discriminant Analysis	flexdaCMA
Flexible Discriminant Analysis	flexdaCMA,data.frame,missing,formula-method flexdaCMA,ExpressionSet,character,missing-method flexdaCMA,matrix,factor,missing-method flexdaCMA,matrix,numeric,missing-method flexdaCMA-methods
Cross-tabulation of predicted and true class labels	ftable,cloutput-method
Tree-based Gradient Boosting	gbmCMA
Tree-based Gradient Boosting	gbmCMA,data.frame,missing,formula-method gbmCMA,ExpressionSet,character,missing-method gbmCMA,matrix,factor,missing-method gbmCMA,matrix,numeric,missing-method gbmCMA-methods
Repeated Divisions into learn- and tets sets	GenerateLearningsets
"genesel"	genesel genesel-class show,genesel-method
General method for variable selection with various methods	GeneSelection
General method for variable selection with various methods	GeneSelection,data.frame,missing,formula-method GeneSelection,ExpressionSet,character,missing-method GeneSelection,matrix,factor,missing-method GeneSelection,matrix,numeric,missing-method GeneSelection-methods
ALL/AML dataset of Golub et al. (1999)	golub
Internal functions	bklr bklr.predict bkreg care.dev care.exp characterplot mklr mklr.predict mkreg my.care.exp plotprob ROCinternal roundvector rowswaps safeexp
Combine list elements returned by the method classification	join
Combine list elements returned by the method classification	join,list-method join-methods
Small blue round cell tumor dataset of Khan et al. (2001)	khan
Nearest Neighbours	knnCMA
Nearest Neighbours	knnCMA,data.frame,missing,formula-method knnCMA,ExpressionSet,character,missing-method knnCMA,matrix,factor,missing-method knnCMA,matrix,numeric,missing-method knnCMA-methods
L1 penalized logistic regression	LassoCMA
L1 penalized logistic regression	LassoCMA,data.frame,missing,formula-method LassoCMA,ExpressionSet,character,missing-method LassoCMA,matrix,factor,missing-method LassoCMA,matrix,numeric,missing-method LassoCMA-methods
Linear Discriminant Analysis	ldaCMA
Linear Discriminant Analysis	ldaCMA,data.frame,missing,formula-method ldaCMA,ExpressionSet,character,missing-method ldaCMA,matrix,factor,missing-method ldaCMA,matrix,numeric,missing-method ldaCMA-methods
"learningsets"	learningsets learningsets-class show,learningsets-method
Feed-forward Neural Networks	nnetCMA
Feed-Forward Neural Networks	nnetCMA,data.frame,missing,formula-method nnetCMA,ExpressionSet,character,missing-method nnetCMA,matrix,factor,missing-method nnetCMA,matrix,numeric,missing-method nnetCMA-methods
Classifiability of observations	obsinfo
Probabilistic Nearest Neighbours	pknnCMA
Probabilistic nearest neighbours	pknnCMA,data.frame,missing,formula-method pknnCMA,ExpressionSet,character,missing-method pknnCMA,matrix,factor,missing-method pknnCMA,matrix,numeric,missing-method pknnCMA-methods
Visualize Separability of different classes	Planarplot
Visualize Separability of different classes	Planarplot,data.frame,missing,formula-method Planarplot,ExpressionSet,character,missing-method Planarplot,matrix,factor,missing-method Planarplot,matrix,numeric,missing-method Planarplot-methods
Probability plot	plot,cloutput,missing-method plot,cloutput-method
Visualize results of tuning	plot,tuningresult,missing-method plot,tuningresult-method
L2 penalized logistic regression	plrCMA
L2 penalized logistic regression	plrCMA,data.frame,missing,formula-method plrCMA,ExpressionSet,character,missing-method plrCMA,matrix,factor,missing-method plrCMA,matrix,numeric,missing-method plrCMA-methods
Partial Least Squares combined with Linear Discriminant Analysis	pls_ldaCMA
Partial Least Squares combined with Linear Discriminant Analysis	pls_ldaCMA,data.frame,missing,formula-method pls_ldaCMA,ExpressionSet,character,missing-method pls_ldaCMA,matrix,factor,missing-method pls_ldaCMA,matrix,numeric,missing-method pls_ldaCMA-methods
Partial Least Squares followed by logistic regression	pls_lrCMA
Partial Least Squares followed by logistic regression	pls_lrCMA,data.frame,missing,formula-method pls_lrCMA,ExpressionSet,character,missing-method pls_lrCMA,matrix,factor,missing-method pls_lrCMA,matrix,numeric,missing-method pls_lrCMA-methods
Partial Least Squares followed by random forests	pls_rfCMA
Partial Least Squares followed by random forests	pls_rfCMA,data.frame,missing,formula-method pls_rfCMA,ExpressionSet,character,missing-method pls_rfCMA,matrix,factor,missing-method pls_rfCMA,matrix,numeric,missing-method pls_rfCMA-methods
Probabilistic Neural Networks	pnnCMA
Probabilistic Neural Networks	pnnCMA,data.frame,missing,formula-method pnnCMA,ExpressionSet,character,missing-method pnnCMA,matrix,factor,missing-method pnnCMA,matrix,numeric,missing-method pnnCMA-methods
General method for predicting classes of new observations	prediction
General method for predicting class lables of new observations	prediction,data.frame,missing,data.frame,formula-method prediction,ExpressionSet,character,ExpressionSet,missing-method prediction,matrix,ANY,matrix,missing-method prediction-methods
"predoutput"	predoutput predoutput-class show,predoutput-method
Quadratic Discriminant Analysis	qdaCMA
Quadratic Discriminant Analysis	qdaCMA,data.frame,missing,formula-method qdaCMA,ExpressionSet,character,missing-method qdaCMA,matrix,factor,missing-method qdaCMA,matrix,numeric,missing-method qdaCMA-methods
Classification based on Random Forests	rfCMA
Classification based on Random Forests	rfCMA,data.frame,missing,formula-method rfCMA,ExpressionSet,character,missing-method rfCMA,matrix,factor,missing-method rfCMA,matrix,numeric,missing-method rfCMA-methods
Receiver Operator Characteristic	roc roc,cloutput-method
Shrunken Centroids Discriminant Analysis	scdaCMA
Shrunken Centroids Discriminant Analysis	scdaCMA,data.frame,missing,formula-method scdaCMA,ExpressionSet,character,missing-method scdaCMA,matrix,factor,missing-method scdaCMA,matrix,numeric,missing-method scdaCMA-methods
Shrinkage linear discriminant analysis	shrinkldaCMA
Shrinkage linear discriminant analysis	shrinkldaCMA,data.frame,missing,formula-method shrinkldaCMA,ExpressionSet,character,missing-method shrinkldaCMA,matrix,factor,missing-method shrinkldaCMA,matrix,numeric,missing-method shrinkldaCMA-methods
Summarize classifier evaluation	summary,evaloutput-method
Support Vector Machine	svmCMA
Support Vector Machine	svmCMA,data.frame,missing,formula-method svmCMA,ExpressionSet,character,missing-method svmCMA,matrix,factor,missing-method svmCMA,matrix,numeric,missing-method svmCMA-methods
Display 'top' variables	toplist toplist,genesel-method
Hyperparameter tuning for classifiers	tune
Hyperparameter tuning for classifiers	tune,data.frame,missing,formula-method tune,ExpressionSet,character,missing-method tune,matrix,factor,missing-method tune,matrix,numeric,missing-method tune-methods
"tuningresult"	show,tuningresult-method tuningresult tuningresult-class
"varseloutput"	varseloutput varseloutput-class
Tuning / Selection bias correction	weighted.mcr
General method for tuning / selection bias correction	weighted.mcr,character,character,missing,character,matrix,factor-method weighted.mcr,character,character,numeric,character,matrix,factor-method weighted.mcr,character,character,numeric,character,matrix,numeric-method weighted.mcr-methods
Tuning / Selection bias correction based on matrix of subsampling fold errors	wmc
General method for tuning / selection bias correction based on a matrix of subsampling fold errors.	wmc,matrix,numeric,numeric-method wmc-methods
"wmcr.result"	show,wmcr.result-method wmcr.result wmcr.result-class