Man pages for CMA
Synthesis of microarray-based classification

bestShow best hyperparameter settings
boxplotMake a boxplot of the classifier evaluation
classificationGeneral method for classification with various methods
classification-methodsGeneral method for classification with various methods
cloutput-class"cloutput"
clvarseloutput-class"clvarseloutput"
CMA-packageSynthesis of microarray-based classification
compareCompare different classifiers
compare-methodsCompare different classifiers
compBoostCMAComponentwise Boosting
compBoostCMA-methodsComponentwise Boosting
dldaCMADiagonal Discriminant Analysis
dldaCMA-methodsDiagonal Discriminant Analysis
ElasticNetCMAClassfication and variable selection by the ElasticNet
ElasticNetCMA-methodsClassfication and variable selection by the ElasticNet
evaloutput-class"evaloutput"
evaluationEvaluation of classifiers
evaluation-methodsEvaluation of classifiers
fdaCMAFisher's Linear Discriminant Analysis
fdaCMA-methodsFisher's Linear Discriminant Analysis
filterFilter functions for Gene Selection
flexdaCMAFlexible Discriminant Analysis
flexdaCMA-methodsFlexible Discriminant Analysis
ftableCross-tabulation of predicted and true class labels
gbmCMATree-based Gradient Boosting
gbmCMA-methodsTree-based Gradient Boosting
GenerateLearningsetsRepeated Divisions into learn- and tets sets
genesel-class"genesel"
GeneSelectionGeneral method for variable selection with various methods
GeneSelection-methodsGeneral method for variable selection with various methods
golubALL/AML dataset of Golub et al. (1999)
internalsInternal functions
joinCombine list elements returned by the method classification
join-methodsCombine list elements returned by the method classification
khanSmall blue round cell tumor dataset of Khan et al. (2001)
knnCMANearest Neighbours
knnCMA-methodsNearest Neighbours
LassoCMAL1 penalized logistic regression
LassoCMA-methodsL1 penalized logistic regression
ldaCMALinear Discriminant Analysis
ldaCMA-methodsLinear Discriminant Analysis
learningsets-class"learningsets"
nnetCMAFeed-forward Neural Networks
nnetCMA-methodsFeed-Forward Neural Networks
obsinfoClassifiability of observations
pknnCMAProbabilistic Nearest Neighbours
pknnCMA-methodsProbabilistic nearest neighbours
PlanarplotVisualize Separability of different classes
Planarplot-methodsVisualize Separability of different classes
plot,cloutput-methodProbability plot
plot,genesel-methodBarplot of variable importance
plot,tuningresult-methodVisualize results of tuning
plrCMAL2 penalized logistic regression
plrCMA-methodsL2 penalized logistic regression
pls_ldaCMAPartial Least Squares combined with Linear Discriminant...
pls_ldaCMA-methodsPartial Least Squares combined with Linear Discriminant...
pls_lrCMAPartial Least Squares followed by logistic regression
pls_lrCMA-methodsPartial Least Squares followed by logistic regression
pls_rfCMAPartial Least Squares followed by random forests
pls_rfCMA-methodsPartial Least Squares followed by random forests
pnnCMAProbabilistic Neural Networks
pnnCMA-methodsProbabilistic Neural Networks
predictionGeneral method for predicting classes of new observations
prediction-methodsGeneral method for predicting class lables of new...
predoutput-class"predoutput"
qdaCMAQuadratic Discriminant Analysis
qdaCMA-methodsQuadratic Discriminant Analysis
rfCMAClassification based on Random Forests
rfCMA-methodsClassification based on Random Forests
rocReceiver Operator Characteristic
scdaCMAShrunken Centroids Discriminant Analysis
scdaCMA-methodsShrunken Centroids Discriminant Analysis
shrinkldaCMAShrinkage linear discriminant analysis
shrinkldaCMA-methodsShrinkage linear discriminant analysis
summarySummarize classifier evaluation
svmCMASupport Vector Machine
svmCMA-methodsSupport Vector Machine
toplistDisplay 'top' variables
tuneHyperparameter tuning for classifiers
tune-methodsHyperparameter tuning for classifiers
tuningresult-class"tuningresult"
varseloutput-class"varseloutput"
weighted_mcrTuning / Selection bias correction
weighted_mcr-methodsGeneral method for tuning / selection bias correction
wmcTuning / Selection bias correction based on matrix of...
wmc-methodsGeneral method for tuning / selection bias correction based...
wmcr_result-class"wmcr.result"
CMA documentation built on Nov. 1, 2018, 5:01 a.m.