addLegend	addLegend
addLegend_v1	addLegend_v1
addMarkers	addMarkers
andy2011params	AnnotationParams-class
AnnotationParams	AnnotationParams-class
AnnotationParams-class	AnnotationParams-class
checkFeatureNamesOverlap	checkFeatureNamesOverlap
checkFvarOverlap	checkFvarOverlap
chi2	chi2-methods
chi2,matrix,matrix-method	chi2-methods
chi2,matrix,numeric-method	chi2-methods
chi2,numeric,matrix-method	chi2-methods
chi2,numeric,numeric-method	chi2-methods
chi2-methods	chi2-methods
class:AnnotationParams	AnnotationParams-class
class:GenRegRes	GenRegRes-class
class:ThetaRegRes	GenRegRes-class
combineThetaRegRes	GenRegRes-class
dunkley2006params	AnnotationParams-class
empPvalues	empPvalues
exprsToRatios	exprsToRatios-methods
exprsToRatios,MSnSet-method	exprsToRatios-methods
exprsToRatios-methods	exprsToRatios-methods
f1Count	GenRegRes-class
f1Count,GenRegRes-method	GenRegRes-class
f1Count,ThetaRegRes-method	GenRegRes-class
favourPrimary	GenRegRes-class
filterBinMSnSet	filterBinMSnSet
filterZeroCols	filterZeroCols
filterZeroRows	filterZeroCols
GenRegRes	GenRegRes-class
GenRegRes-class	GenRegRes-class
getAnnotationParams	AnnotationParams-class
getF1Scores	GenRegRes-class
getF1Scores,GenRegRes-method	GenRegRes-class
getF1Scores,ThetaRegRes-method	GenRegRes-class
getGOEvidenceCodes	showGOEvidenceCodes
getGOFromFeatures	getGOFromFeatures
getMarkerClasses	getMarkerClasses
getMarkers	getMarkers
getParams	GenRegRes-class
getParams,ClustRegRes-method	undocumented
getParams,GenRegRes-method	GenRegRes-class
getParams,ThetaRegRes-method	GenRegRes-class
getPredictions	getPredictions
getRegularisedParams	GenRegRes-class
getRegularisedParams,GenRegRes-method	GenRegRes-class
getRegularizedParams	GenRegRes-class
getRegularizedParams,GenRegRes-method	GenRegRes-class
getSeed	GenRegRes-class
getSeed,GenRegRes-method	GenRegRes-class
getStockcol	getStockcol
getStockpch	getStockcol
getUnknowncol	getStockcol
getUnknownpch	getStockcol
getWarnings	GenRegRes-class
getWarnings,GenRegRes-method	GenRegRes-class
highlightOnPlot	highlightOnPlot
knnClassification	knnClassification
knnOptimisation	knnOptimisation
knnOptimization	knnOptimisation
knnPrediction	knnClassification
knnRegularisation	knnOptimisation
knntlClassification	knntlClassification
knntlOptimisation	knntlOptimisation
ksvmClassification	ksvmClassification
ksvmOptimisation	ksvmOptimisation
ksvmOptimization	ksvmOptimisation
ksvmPrediction	ksvmClassification
ksvmRegularisation	ksvmOptimisation
levelPlot	GenRegRes-class
levelPlot,ClustRegRes-method	undocumented
levelPlot,GenRegRes-method	GenRegRes-class
lopims	lopims
lopims1	lopims
lopims2	lopims
lopims3	lopims
lopims4	lopims
lopims5	lopims
makeGoSet	makeGoSet
makeNaData	makeNaData
makeNaData2	makeNaData
markerMSnSet	markerMSnSet
minClassScore	minClassScore
minMarkers	minMarkers
MLearn,formula,MSnSet,clusteringSchema,missing-method	MLearn-methods
MLearn,formula,MSnSet,learnerSchema,numeric-method	MLearn-methods
MLearn,formula,MSnSet,learnerSchema,xvalSpec-method	MLearn-methods
MLearnMSnSet	MLearn-methods
MSnSetMLean	MLearn-methods
nbClassification	nbClassification
nbOptimisation	nbOptimisation
nbOptimization	nbOptimisation
nbPrediction	nbClassification
nbRegularisation	nbOptimisation
nndist	nndist-methods
nndist,matrix,matrix-method	nndist-methods
nndist,matrix,missing-method	nndist-methods
nndist,MSnSet,missing-method	nndist-methods
nndist-methods	nndist-methods
nnetClassification	nnetClassification
nnetOptimisation	nnetOptimisation
nnetOptimization	nnetOptimisation
nnetPrediction	nnetClassification
nnetRegularisation	nnetOptimisation
perTurboClassification	perTurboClassification
perTurboOptimisation	perTurboOptimisation
perTurboOptimization	perTurboOptimisation
phenoDisco	phenoDisco
plot,ClustRegRes,missing-method	undocumented
plot,GenRegRes,missing-method	GenRegRes-class
plot,ThetaRegRes,missing-method	GenRegRes-class
plot2D	plot2D
plot2D_v1	plot2D_v1
plotDist	plotDist
plsdaClassification	plsdaClassification
plsdaOptimisation	plsdaOptimisation
plsdaOptimization	plsdaOptimisation
plsdaPrediction	plsdaClassification
plsdaRegularisation	plsdaOptimisation
pRolocmarkers	pRolocmarkers
rfClassification	rfClassification
rfOptimisation	rfOptimisation
rfOptimization	rfOptimisation
rfPrediction	rfClassification
rfRegularisation	rfOptimisation
sampleMSnSet	sampleMSnSet
setAnnotationParams	AnnotationParams-class
setStockcol	getStockcol
setStockpch	getStockcol
setUnknowncol	getStockcol
setUnknownpch	getStockcol
show,AnnotationParams-method	AnnotationParams-class
show,ClustRegRes-method	undocumented
show,GenRegRes-method	GenRegRes-class
show,ThetaRegRes-method	GenRegRes-class
showGOEvidenceCodes	showGOEvidenceCodes
svmClassification	svmClassification
svmOptimisation	svmOptimisation
svmOptimization	svmOptimisation
svmPrediction	svmClassification
svmRegularisation	svmOptimisation
testMarkers	testMarkers
testMSnSet	testMSnSet
ThetaRegRes	GenRegRes-class
ThetaRegRes-class	GenRegRes-class
thetas	thetas
undocumented	undocumented
unknownMSnSet	markerMSnSet
whichNA	makeNaData
