CoGAPS-package	CoGAPS-package
binaryA	binaryA-methods
binaryA,CogapsResult-method	binaryA-methods
buildReport	buildReport
calcCoGAPSStat	calcCoGAPSStat-methods
calcCoGAPSStat,CogapsResult-method	calcCoGAPSStat-methods
calcGeneGSStat	calcGeneGSStat-methods
calcGeneGSStat,CogapsResult-method	calcGeneGSStat-methods
calcZ	calcZ-methods
calcZ,CogapsResult-method	calcZ-methods
callInternalCoGAPS	callInternalCoGAPS
checkDataMatrix	checkDataMatrix
checkInputs	checkInputs
checkpointsEnabled	checkpointsEnabled
CoGAPS	CoGAPS
CogapsParams	CogapsParams
CogapsParams-class	CogapsParams-class
CogapsResult-class	CogapsResult-class
compiledWithOpenMPSupport	compiledWithOpenMPSupport
computeGeneGSProb	computeGeneGSProb-methods
computeGeneGSProb,CogapsResult-method	computeGeneGSProb-methods
convertDataToMatrix	convertDataToMatrix
corcut	corcut
corrToMeanPattern	corrToMeanPattern
createCogapsResult	createCogapsResult
createSets	createSets
distributedCogaps	distributedCogaps
findConsensusMatrix	findConsensusMatrix
fromCSV	fromCSV-methods
fromCSV,character-method	fromCSV-methods
gapsCat	gapsCat
getAmplitudeMatrix	getAmplitudeMatrix-methods
getAmplitudeMatrix,CogapsResult-method	getAmplitudeMatrix-methods
getClusteredPatterns	getClusteredPatterns-methods
getClusteredPatterns,CogapsResult-method	getClusteredPatterns-methods
getCorrelationToMeanPattern	getCorrelationToMeanPattern-methods
getCorrelationToMeanPattern,CogapsResult-method	getCorrelationToMeanPattern-methods
getDimNames	getDimNames
getFeatureLoadings	getFeatureLoadings-methods
getFeatureLoadings,CogapsResult-method	getFeatureLoadings-methods
getGeneNames	getGeneNames
getMeanChiSq	getMeanChiSq-methods
getMeanChiSq,CogapsResult-method	getMeanChiSq-methods
getOriginalParameters	getOriginalParameters-methods
getOriginalParameters,CogapsResult-method	getOriginalParameters-methods
getParam	getParam-methods
getParam,CogapsParams-method	getParam-methods
getPatternGeneSet	getPatternGeneSet-methods
getPatternGeneSet,CogapsResult,list,character-method	getPatternGeneSet-methods
getPatternMatrix	getPatternMatrix-methods
getPatternMatrix,CogapsResult-method	getPatternMatrix-methods
getRetinaSubset	getRetinaSubset
getSampleFactors	getSampleFactors-methods
getSampleFactors,CogapsResult-method	getSampleFactors-methods
getSampleNames	getSampleNames
getSubsets	getSubsets-methods
getSubsets,CogapsResult-method	getSubsets-methods
getUnmatchedPatterns	getUnmatchedPatterns-methods
getUnmatchedPatterns,CogapsResult-method	getUnmatchedPatterns-methods
getValueOrRds	getValueOrRds
getVersion	getVersion-methods
getVersion,CogapsResult-method	getVersion-methods
GIST.data_frame	GIST.data_frame
GIST.matrix	GIST.matrix
GIST.result	GIST.result
GIST.uncertainty	GIST.uncertainty
GWCoGAPS	GWCoGAPS
initialize,CogapsParams-method	initialize-CogapsParams-method
initialize,CogapsResult-method	initialize-CogapsResult-method
isRdsFile	isRdsFile
MANOVA	MANOVA-methods
MANOVA,matrix,CogapsResult-method	MANOVA-methods
modsimdata	modsimdata
modsimresult	modsimresult
ncolHelper	ncolHelper
nrowHelper	nrowHelper
parseExtraParams	parseExtraParams
patternMarkers	patternMarkers-methods
patternMarkers,CogapsResult-method	patternMarkers-methods
patternMatch	patternMatch
plotPatternGeneSet	plotPatternGeneSet-methods
plotPatternGeneSet,list,numeric,numeric-method	plotPatternGeneSet-methods
plotPatternMarkers	plotPatternMarkers-methods
plotResiduals	plotResiduals-methods
plotResiduals,CogapsResult-method	plotResiduals-methods
reconstructGene	reconstructGene-methods
reconstructGene,CogapsResult-method	reconstructGene-methods
sampleUniformly	sampleUniformly
sampleWithAnnotationWeights	sampleWithAnnotationWeights
sampleWithExplictSets	sampleWithExplictSets
scCoGAPS	scCoGAPS
setAnnotationWeights	setAnnotationWeights-methods
setAnnotationWeights,CogapsParams-method	setAnnotationWeights-methods
setDistributedParams	setDistributedParams-methods
setDistributedParams,CogapsParams-method	setDistributedParams-methods
setFixedPatterns	setFixedPatterns-methods
setFixedPatterns,CogapsParams-method	setFixedPatterns-methods
setParam	setParam-methods
setParam,CogapsParams-method	setParam-methods
startupMessage	startupMessage
stitchTogether	stitchTogether
supported	supported
toCSV	toCSV-methods
toCSV,CogapsResult,character-method	toCSV-methods
