addGoAnnotations	addGoAnnotations
addLegend	addLegend
addMarkers	addMarkers
andy2011params	AnnotationParams-class
AnnotationParams	AnnotationParams-class
AnnotationParams-class	AnnotationParams-class
as.data.frame.MartInstance	MartInstance-class
as.data.frame.MartInstanceList	MartInstance-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::QSep	QSep-class
class:AnnotationParams	AnnotationParams-class
class:ClustDist	ClustDist-class
class:ClustDistList	ClustDistList-class
class:GenRegRes	GenRegRes-class
class:SpatProtVis	SpatProtVis-class
class:ThetaRegRes	GenRegRes-class
classWeights	classWeights
ClustDist	ClustDist-class
clustDist	clustDist
ClustDist-class	ClustDist-class
ClustDistList	ClustDistList-class
ClustDistList-class	ClustDistList-class
col1	plot2Ds
col2	plot2Ds
combineThetaRegRes	GenRegRes-class
data1	plot2Ds
data2	plot2Ds
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
fDataToUnknown	fDataToUnknown
filterAttrs	MartInstance-class
filterBinMSnSet	filterBinMSnSet
filterMaxMarkers	filterMaxMarkers
filterMinMarkers	filterMinMarkers
filterZeroCols	filterZeroCols
filterZeroRows	filterZeroCols
flipGoTermId	goIdToTerm
GenRegRes	GenRegRes-class
GenRegRes-class	GenRegRes-class
getAnnotationParams	AnnotationParams-class
getF1Scores	GenRegRes-class
getF1Scores,GenRegRes-method	GenRegRes-class
getF1Scores,ThetaRegRes-method	GenRegRes-class
getFilterList	MartInstance-class
getGOEvidenceCodes	showGOEvidenceCodes
getGOFromFeatures	getGOFromFeatures
getLisacol	getStockcol
getMarkerClasses	getMarkerClasses
getMarkers	getMarkers
getMartInstanceList	MartInstance-class
getMartTab	MartInstance-class
getNormDist	getNormDist
getOldcol	getStockcol
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
goIdToTerm	goIdToTerm
goTermToId	goIdToTerm
highlightOnPlot	highlightOnPlot
highlightOnPlot3D	highlightOnPlot
isMrkMat	markers
isMrkVec	markers
knnClassification	knnClassification
knnOptimisation	knnOptimisation
knnOptimization	knnOptimisation
knnPrediction	knnClassification
knnRegularisation	knnOptimisation
knntlClassification	knntlClassification
knntlOptimisation	knntlOptimisation
ksvmClassification	ksvmClassification
ksvmOptimisation	ksvmOptimisation
ksvmOptimization	ksvmOptimisation
ksvmPrediction	ksvmClassification
ksvmRegularisation	ksvmOptimisation
lapply,ClustDistList-method	ClustDistList-class
lapply,MartInstanceList,ANY-method	MartInstance-class
lapply,MartInstanceList-method	MartInstance-class
length,ClustDistList-method	ClustDistList-class
levelPlot	GenRegRes-class
levelPlot,ClustRegRes-method	undocumented
levelPlot,GenRegRes-method	GenRegRes-class
levelPlot,QSep-method	QSep-class
lopims	lopims
lopims1	lopims
lopims2	lopims
lopims3	lopims
lopims4	lopims
lopims5	lopims
makeGoSet	makeGoSet
markerMSnSet	markerMSnSet
markers	markers
MartInstance	MartInstance-class
MartInstance-class	MartInstance-class
MartInstanceList	MartInstance-class
MartInstanceList-class	MartInstance-class
minClassScore	defunct
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
move2Ds	move2Ds
mrkConsProfiles	mrkConsProfiles
mrkEncoding	markers
mrkHClust	mrkHClust
mrkMatAndVec	markers
mrkMatToVec	markers
mrkVecToMat	markers
MSnSetMLean	MLearn-methods
names,ClustDistList-method	ClustDistList-class
names,QSep-method	QSep-class
names<-,ClustDistList,ANY-method	ClustDistList-class
names<-,QSep,character-method	QSep-class
nbClassification	nbClassification
nbOptimisation	nbOptimisation
nbOptimization	nbOptimisation
nbPrediction	nbClassification
nbRegularisation	nbOptimisation
nDatasets	MartInstance-class
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
orderGoAnnotations	orderGoAnnotations
orgQuants	orgQuants
perTurboClassification	perTurboClassification
perTurboOptimisation	perTurboOptimisation
perTurboOptimization	perTurboOptimisation
phenoDisco	phenoDisco
plot,ClustDist,MSnSet-method	ClustDist-class
plot,ClustDistList,missing-method	ClustDistList-class
plot,ClustRegRes,missing-method	undocumented
plot,GenRegRes,missing-method	GenRegRes-class
plot,QSep,missing-method	QSep-class
plot,QSep-method	QSep-class
plot,SpatProtVis,missing-method	SpatProtVis-class
plot,ThetaRegRes,missing-method	GenRegRes-class
plot2D	plot2D
plot2Dmethods	plot2D
plot2Ds	plot2Ds
plot3D,MSnSet-method	plot2D
plotDist	plotDist
plsdaClassification	plsdaClassification
plsdaOptimisation	plsdaOptimisation
plsdaOptimization	plsdaOptimisation
plsdaPrediction	plsdaClassification
plsdaRegularisation	plsdaOptimisation
prettyGoTermId	goIdToTerm
pRoloc-defunct	defunct
pRoloc-deprecated	defunct
pRolocmarkers	pRolocmarkers
QSep	QSep-class
qsep	QSep-class
QSep-class	QSep-class
rfClassification	rfClassification
rfOptimisation	rfOptimisation
rfOptimization	rfOptimisation
rfPrediction	rfClassification
rfRegularisation	rfOptimisation
sampleMSnSet	sampleMSnSet
sapply,ClustDistList-method	ClustDistList-class
sapply,MartInstanceList,ANY-method	MartInstance-class
sapply,MartInstanceList-method	MartInstance-class
setAnnotationParams	AnnotationParams-class
setLisacol	getStockcol
setOldcol	getStockcol
setStockcol	getStockcol
setStockpch	getStockcol
setUnknowncol	getStockcol
setUnknownpch	getStockcol
show,AnnotationParams-method	AnnotationParams-class
show,ClustDist-method	ClustDist-class
show,ClustDistList-method	ClustDistList-class
show,ClustRegRes-method	undocumented
show,GenRegRes-method	GenRegRes-class
show,MartInstance-method	MartInstance-class
show,QSep-method	QSep-class
show,SpatProtVis-method	SpatProtVis-class
show,ThetaRegRes-method	GenRegRes-class
showGOEvidenceCodes	showGOEvidenceCodes
showMrkMat	markers
SpatProtVis	SpatProtVis-class
SpatProtVis-class	SpatProtVis-class
subsetMarkers	subsetMarkers
summary,QSep-method	QSep-class
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
zerosInBinMSnSet	zerosInBinMSnSet
[,ClustDistList,ANY,ANY,ANY-method	ClustDistList-class
[,ClustDistList,ANY,missing,missing-method	ClustDistList-class
[,MartInstanceList,ANY,ANY,ANY-method	MartInstance-class
[,MartInstanceList,ANY,ANY-method	MartInstance-class
[,MartInstanceList-method	MartInstance-class
[[,ClustDistList,ANY,ANY-method	ClustDistList-class
[[,ClustDistList,ANY,missing-method	ClustDistList-class
[[,MartInstanceList,ANY,ANY-method	MartInstance-class
[[,MartInstanceList-method	MartInstance-class
