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.

AuthorMartin Slawski <ms@cs.uni-sb.de>, Anne-Laure Boulesteix <boulesteix@ibe.med.uni-muenchen.de>, Christoph Bernau <bernau@ibe.med.uni-muenchen.de>.
Date of publicationNone
MaintainerChristoph Bernau <bernau@ibe.med.uni-muenchen.de>
LicenseGPL (>= 2)
Version1.32.0

View on Bioconductor

Man pages

best: Show best hyperparameter settings

boxplot: Make a boxplot of the classifier evaluation

classification: General method for classification with various methods

classification-methods: General method for classification with various methods

cloutput-class: "cloutput"

clvarseloutput-class: "clvarseloutput"

CMA-package: Synthesis of microarray-based classification

compare: Compare different classifiers

compare-methods: Compare different classifiers

compBoostCMA: Componentwise Boosting

compBoostCMA-methods: Componentwise Boosting

dldaCMA: Diagonal Discriminant Analysis

dldaCMA-methods: Diagonal Discriminant Analysis

ElasticNetCMA: Classfication and variable selection by the ElasticNet

ElasticNetCMA-methods: Classfication and variable selection by the ElasticNet

evaloutput-class: "evaloutput"

evaluation: Evaluation of classifiers

evaluation-methods: Evaluation of classifiers

fdaCMA: Fisher's Linear Discriminant Analysis

fdaCMA-methods: Fisher's Linear Discriminant Analysis

flexdaCMA: Flexible Discriminant Analysis

flexdaCMA-methods: Flexible Discriminant Analysis

ftable: Cross-tabulation of predicted and true class labels

gbmCMA: Tree-based Gradient Boosting

gbmCMA-methods: Tree-based Gradient Boosting

GenerateLearningsets: Repeated Divisions into learn- and tets sets

genesel-class: "genesel"

GeneSelection: General method for variable selection with various methods

GeneSelection-methods: General method for variable selection with various methods

golub: ALL/AML dataset of Golub et al. (1999)

join: Combine list elements returned by the method classification

join-methods: Combine list elements returned by the method classification

khan: Small blue round cell tumor dataset of Khan et al. (2001)

knnCMA: Nearest Neighbours

knnCMA-methods: Nearest Neighbours

LassoCMA: L1 penalized logistic regression

LassoCMA-methods: L1 penalized logistic regression

ldaCMA-methods: Linear Discriminant Analysis

learningsets-class: "learningsets"

nnetCMA: Feed-forward Neural Networks

nnetCMA-methods: Feed-Forward Neural Networks

obsinfo: Classifiability of observations

pknnCMA: Probabilistic Nearest Neighbours

pknnCMA-methods: Probabilistic nearest neighbours

Planarplot: Visualize Separability of different classes

Planarplot-methods: Visualize Separability of different classes

plot,cloutput-method: Probability plot

plot,genesel-method: Barplot of variable importance

plot,tuningresult-method: Visualize results of tuning

plrCMA: L2 penalized logistic regression

plrCMA-methods: L2 penalized logistic regression

pls_ldaCMA: Partial Least Squares combined with Linear Discriminant...

pls_ldaCMA-methods: Partial Least Squares combined with Linear Discriminant...

pls_lrCMA-methods: Partial Least Squares followed by logistic regression

pls_rfCMA: Partial Least Squares followed by random forests

pls_rfCMA-methods: Partial Least Squares followed by random forests

pnnCMA-methods: Probabilistic Neural Networks

prediction: General method for predicting classes of new observations

prediction-methods: General method for predicting class lables of new...

predoutput-class: "predoutput"

qdaCMA-methods: Quadratic Discriminant Analysis

rfCMA: Classification based on Random Forests

rfCMA-methods: Classification based on Random Forests

roc: Receiver Operator Characteristic

scdaCMA-methods: Shrunken Centroids Discriminant Analysis

shrinkldaCMA: Shrinkage linear discriminant analysis

shrinkldaCMA-methods: Shrinkage linear discriminant analysis

summary: Summarize classifier evaluation

svmCMA: Support Vector Machine

svmCMA-methods: Support Vector Machine

toplist: Display 'top' variables

tune: Hyperparameter tuning for classifiers

tune-methods: Hyperparameter tuning for classifiers

tuningresult-class: "tuningresult"

varseloutput-class: "varseloutput"

weighted_mcr: Tuning / Selection bias correction

weighted_mcr-methods: General method for tuning / selection bias correction

wmc: Tuning / Selection bias correction based on matrix of...

wmc-methods: General method for tuning / selection bias correction based...

wmcr_result-class: "wmcr.result"

Functions

best Man page
best,tuningresult-method Man page
boxplot,evaloutput-method Man page
classification Man page
classification,data.frame,missing,formula-method Man page
classification,ExpressionSet,character,missing-method Man page
classification,matrix,factor,missing-method Man page
classification,matrix,numeric,missing-method Man page
classification-methods Man page
cloutput Man page
cloutput-class Man page
clvarseloutput Man page
clvarseloutput-class Man page
CMA Man page
CMA-package Man page
compare Man page
compare,list-method Man page
compare-methods Man page
compBoostCMA Man page
compBoostCMA,data.frame,missing,formula-method Man page
compBoostCMA,ExpressionSet,character,missing-method Man page
compBoostCMA,matrix,factor,missing-method Man page
compBoostCMA,matrix,numeric,missing-method Man page
compBoostCMA-methods Man page
dldaCMA Man page
dldaCMA,data.frame,missing,formula-method Man page
dldaCMA,ExpressionSet,character,missing-method Man page
dldaCMA,matrix,factor,missing-method Man page
dldaCMA,matrix,numeric,missing-method Man page
dldaCMA-methods Man page
ElasticNetCMA Man page
ElasticNetCMA,data.frame,missing,formula-method Man page
ElasticNetCMA,ExpressionSet,character,missing-method Man page
ElasticNetCMA,matrix,factor,missing-method Man page
ElasticNetCMA,matrix,numeric,missing-method Man page
ElasticNetCMA-methods Man page
evaloutput Man page
evaloutput-class Man page
evaluation Man page
evaluation,list-method Man page
evaluation-methods Man page
fdaCMA Man page
fdaCMA,data.frame,missing,formula-method Man page
fdaCMA,ExpressionSet,character,missing-method Man page
fdaCMA,matrix,factor,missing-method Man page
fdaCMA,matrix,numeric,missing-method Man page
fdaCMA-methods Man page
flexdaCMA Man page
flexdaCMA,data.frame,missing,formula-method Man page
flexdaCMA,ExpressionSet,character,missing-method Man page
flexdaCMA,matrix,factor,missing-method Man page
flexdaCMA,matrix,numeric,missing-method Man page
flexdaCMA-methods Man page
ftable,cloutput-method Man page
gbmCMA Man page
gbmCMA,data.frame,missing,formula-method Man page
gbmCMA,ExpressionSet,character,missing-method Man page
gbmCMA,matrix,factor,missing-method Man page
gbmCMA,matrix,numeric,missing-method Man page
gbmCMA-methods Man page
GenerateLearningsets Man page
genesel Man page
genesel-class Man page
GeneSelection Man page
GeneSelection,data.frame,missing,formula-method Man page
GeneSelection,ExpressionSet,character,missing-method Man page
GeneSelection,matrix,factor,missing-method Man page
GeneSelection,matrix,numeric,missing-method Man page
GeneSelection-methods Man page
golub Man page
join Man page
join,list-method Man page
join-methods Man page
khan Man page
knnCMA Man page
knnCMA,data.frame,missing,formula-method Man page
knnCMA,ExpressionSet,character,missing-method Man page
knnCMA,matrix,factor,missing-method Man page
knnCMA,matrix,numeric,missing-method Man page
knnCMA-methods Man page
LassoCMA Man page
LassoCMA,data.frame,missing,formula-method Man page
LassoCMA,ExpressionSet,character,missing-method Man page
LassoCMA,matrix,factor,missing-method Man page
LassoCMA,matrix,numeric,missing-method Man page
LassoCMA-methods Man page
ldaCMA,data.frame,missing,formula-method Man page
ldaCMA,ExpressionSet,character,missing-method Man page
ldaCMA,matrix,factor,missing-method Man page
ldaCMA,matrix,numeric,missing-method Man page
ldaCMA-methods Man page
learningsets Man page
learningsets-class Man page
nnetCMA Man page
nnetCMA,data.frame,missing,formula-method Man page
nnetCMA,ExpressionSet,character,missing-method Man page
nnetCMA,matrix,factor,missing-method Man page
nnetCMA,matrix,numeric,missing-method Man page
nnetCMA-methods Man page
obsinfo Man page
obsinfo,evaloutput-method Man page
pknnCMA Man page
pknnCMA,data.frame,missing,formula-method Man page
pknnCMA,ExpressionSet,character,missing-method Man page
pknnCMA,matrix,factor,missing-method Man page
pknnCMA,matrix,numeric,missing-method Man page
pknnCMA-methods Man page
Planarplot Man page
Planarplot,data.frame,missing,formula-method Man page
Planarplot,ExpressionSet,character,missing-method Man page
Planarplot,matrix,factor,missing-method Man page
Planarplot,matrix,numeric,missing-method Man page
Planarplot-methods Man page
plot,cloutput-method Man page
plot,cloutput-method Man page
plot,cloutput,missing-method Man page
plot,genesel-method Man page
plot,genesel,missing-method Man page
plot,tuningresult-method Man page
plot,tuningresult,missing-method Man page
plrCMA Man page
plrCMA,data.frame,missing,formula-method Man page
plrCMA,ExpressionSet,character,missing-method Man page
plrCMA,matrix,factor,missing-method Man page
plrCMA,matrix,numeric,missing-method Man page
plrCMA-methods Man page
pls_ldaCMA Man page
pls_ldaCMA,data.frame,missing,formula-method Man page
pls_ldaCMA,ExpressionSet,character,missing-method Man page
pls_ldaCMA,matrix,factor,missing-method Man page
pls_ldaCMA,matrix,numeric,missing-method Man page
pls_ldaCMA-methods Man page
pls_lrCMA,data.frame,missing,formula-method Man page
pls_lrCMA,ExpressionSet,character,missing-method Man page
pls_lrCMA,matrix,factor,missing-method Man page
pls_lrCMA,matrix,numeric,missing-method Man page
pls_lrCMA-methods Man page
pls_rfCMA Man page
pls_rfCMA,data.frame,missing,formula-method Man page
pls_rfCMA,ExpressionSet,character,missing-method Man page
pls_rfCMA,matrix,factor,missing-method Man page
pls_rfCMA,matrix,numeric,missing-method Man page
pls_rfCMA-methods Man page
pnnCMA,data.frame,missing,formula-method Man page
pnnCMA,ExpressionSet,character,missing-method Man page
pnnCMA,matrix,factor,missing-method Man page
pnnCMA,matrix,numeric,missing-method Man page
pnnCMA-methods Man page
prediction Man page
prediction,data.frame,missing,data.frame,formula-method Man page
prediction,ExpressionSet,character,ExpressionSet,missing-method Man page
prediction,matrix,ANY,matrix,missing-method Man page
prediction-methods Man page
predoutput Man page
predoutput-class Man page
qdaCMA,data.frame,missing,formula-method Man page
qdaCMA,ExpressionSet,character,missing-method Man page
qdaCMA,matrix,factor,missing-method Man page
qdaCMA,matrix,numeric,missing-method Man page
qdaCMA-methods Man page
rfCMA Man page
rfCMA,data.frame,missing,formula-method Man page
rfCMA,ExpressionSet,character,missing-method Man page
rfCMA,matrix,factor,missing-method Man page
rfCMA,matrix,numeric,missing-method Man page
rfCMA-methods Man page
roc Man page
roc,cloutput-method Man page
scdaCMA,data.frame,missing,formula-method Man page
scdaCMA,ExpressionSet,character,missing-method Man page
scdaCMA,matrix,factor,missing-method Man page
scdaCMA,matrix,numeric,missing-method Man page
scdaCMA-methods Man page
show,cloutput-method Man page
show,evaloutput-method Man page
show,genesel-method Man page
show,learningsets-method Man page
show,predoutput-method Man page
show,tuningresult-method Man page
show,wmcr.result-method Man page
shrinkldaCMA Man page
shrinkldaCMA,data.frame,missing,formula-method Man page
shrinkldaCMA,ExpressionSet,character,missing-method Man page
shrinkldaCMA,matrix,factor,missing-method Man page
shrinkldaCMA,matrix,numeric,missing-method Man page
shrinkldaCMA-methods Man page
summary,evaloutput-method Man page
svmCMA Man page
svmCMA,data.frame,missing,formula-method Man page
svmCMA,ExpressionSet,character,missing-method Man page
svmCMA,matrix,factor,missing-method Man page
svmCMA,matrix,numeric,missing-method Man page
svmCMA-methods Man page
toplist Man page
toplist,genesel-method Man page
tune Man page
tune,data.frame,missing,formula-method Man page
tune,ExpressionSet,character,missing-method Man page
tune,matrix,factor,missing-method Man page
tune,matrix,numeric,missing-method Man page
tune-methods Man page
tuningresult Man page
tuningresult-class Man page
varseloutput Man page
varseloutput-class Man page
weighted.mcr Man page
weighted.mcr,character,character,missing,character,matrix,factor Man page
weighted.mcr,character,character,numeric,character,matrix,factor Man page
weighted.mcr,character,character,numeric,character,matrix,numeri Man page
weighted.mcr-methods Man page
wmc Man page
wmc,matrix,numeric,numeric-method Man page
wmc-methods Man page
wmcr.result Man page
wmcr.result-class Man page

Files

CMA/DESCRIPTION
CMA/NAMESPACE
CMA/R
CMA/R/ElasticNetCMA.r
CMA/R/GeneSelection.r
CMA/R/GenerateLearningsets.r
CMA/R/LassoCMA.r
CMA/R/Planarplot.r
CMA/R/classes.r
CMA/R/classification.r
CMA/R/compBoostCMA.r
CMA/R/compare.r
CMA/R/dldaCMA.r
CMA/R/evaluation.r
CMA/R/fdaCMA.r
CMA/R/filter.r
CMA/R/flexdaCMA.r
CMA/R/gbmCMA.r
CMA/R/internals.r
CMA/R/join.r
CMA/R/knnCMA.r
CMA/R/ldaCMA.r
CMA/R/nnetCMA.r
CMA/R/pknnCMA.r
CMA/R/plrCMA.r
CMA/R/pls_ldaCMA.r
CMA/R/pls_lrCMA.r
CMA/R/pls_rfCMA.r
CMA/R/pnnCMA.r
CMA/R/qdaCMA.r
CMA/R/rfCMA.r
CMA/R/scdaCMA.r
CMA/R/shrinkldaCMA.r
CMA/R/svmCMA.r
CMA/R/tune.r
CMA/R/weighted_mcr.r
CMA/R/wmc.r
CMA/build
CMA/build/vignette.rds
CMA/data
CMA/data/golub.rda
CMA/data/khan.rda
CMA/inst
CMA/inst/doc
CMA/inst/doc/CMA_vignette.R
CMA/inst/doc/CMA_vignette.pdf
CMA/inst/doc/CMA_vignette.rnw
CMA/man
CMA/man/CMA-package.Rd CMA/man/ElasticNetCMA-methods.Rd CMA/man/ElasticNetCMA.Rd CMA/man/GeneSelection-methods.Rd CMA/man/GeneSelection.Rd CMA/man/GenerateLearningsets.Rd CMA/man/LassoCMA-methods.Rd CMA/man/LassoCMA.Rd CMA/man/Planarplot-methods.Rd CMA/man/Planarplot.Rd CMA/man/best.Rd CMA/man/boxplot.Rd CMA/man/classification-methods.Rd CMA/man/classification.Rd CMA/man/cloutput-class.Rd CMA/man/clvarseloutput-class.Rd CMA/man/compBoostCMA-methods.Rd CMA/man/compBoostCMA.Rd CMA/man/compare-methods.Rd CMA/man/compare.Rd CMA/man/dldaCMA-methods.Rd CMA/man/dldaCMA.Rd CMA/man/evaloutput-class.Rd CMA/man/evaluation-methods.Rd CMA/man/evaluation.Rd CMA/man/fdaCMA-methods.Rd CMA/man/fdaCMA.Rd
CMA/man/filter.rd
CMA/man/flexdaCMA-methods.Rd CMA/man/flexdaCMA.Rd CMA/man/ftable.Rd CMA/man/gbmCMA-methods.Rd CMA/man/gbmCMA.Rd CMA/man/genesel-class.Rd CMA/man/golub.Rd
CMA/man/internals.rd
CMA/man/join-methods.Rd CMA/man/join.Rd CMA/man/khan.Rd CMA/man/knnCMA-methods.Rd CMA/man/knnCMA.Rd CMA/man/ldaCMA-methods.Rd
CMA/man/ldaCMA.rd
CMA/man/learningsets-class.Rd CMA/man/nnetCMA-methods.Rd CMA/man/nnetCMA.Rd CMA/man/obsinfo.Rd CMA/man/pknnCMA-methods.Rd CMA/man/pknnCMA.Rd CMA/man/plot,cloutput-method.Rd CMA/man/plot,genesel-method.Rd CMA/man/plot,tuningresult-method.Rd CMA/man/plrCMA-methods.Rd CMA/man/plrCMA.Rd CMA/man/pls_ldaCMA-methods.Rd CMA/man/pls_ldaCMA.Rd CMA/man/pls_lrCMA-methods.Rd
CMA/man/pls_lrCMA.rd
CMA/man/pls_rfCMA-methods.Rd CMA/man/pls_rfCMA.Rd CMA/man/pnnCMA-methods.Rd
CMA/man/pnnCMA.rd
CMA/man/prediction-methods.Rd CMA/man/prediction.Rd CMA/man/predoutput-class.Rd CMA/man/qdaCMA-methods.Rd
CMA/man/qdaCMA.rd
CMA/man/rfCMA-methods.Rd CMA/man/rfCMA.Rd CMA/man/roc.Rd CMA/man/scdaCMA-methods.Rd
CMA/man/scdaCMA.rd
CMA/man/shrinkldaCMA-methods.Rd CMA/man/shrinkldaCMA.Rd CMA/man/summary.Rd CMA/man/svmCMA-methods.Rd CMA/man/svmCMA.Rd CMA/man/toplist.Rd CMA/man/tune-methods.Rd CMA/man/tune.Rd CMA/man/tuningresult-class.Rd CMA/man/varseloutput-class.Rd CMA/man/weighted_mcr-methods.Rd CMA/man/weighted_mcr.Rd CMA/man/wmc-methods.Rd CMA/man/wmc.Rd CMA/man/wmcr_result-class.Rd
CMA/vignettes
CMA/vignettes/CMA_vignette.rnw
CMA/vignettes/classification.bib
CMA/vignettes/preamble.tex

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