analysedDataset	analysedDataset
analysedDataset,PhenTestResult-method	PhenTestResult-class
analysedSubset	analysedSubset
analysedSubset,htestPhenStat-method	htestPhenStat-class
analysisResults	analysisResults
analysisResults,PhenTestResult-method	PhenTestResult-class
batchIn	batchIn
batchIn,PhenList-method	batchIn
batchIn,PhenTestResult-method	batchIn
batchIn-methods	batchIn
boxplotResidualBatch	boxplotResidualBatch
boxplotSexGenotype	boxplotSexGenotype
boxplotSexGenotypeBatch	boxplotSexGenotypeBatch
boxplotSexGenotypeBatchAdjusted	boxplotSexGenotypeBatchAdjusted
categoricalBarplot	categoricalBarplot
checkDataset	checkDataset
classificationTag	classificationTag
columnChecks	columnChecks
columnLevels	columnLevels
comparison	comparison
comparison,htestPhenStat-method	htestPhenStat-class
dataset	dataset
dataset,PhenList-method	PhenList-class
determiningLambda	determiningLambda
dim.PhenList	dim
finalLRModel	finalLRModel
finalModel	finalModel
finalTFModel	finalTFModel
FisherExactTest	FisherExactTest
formulaDeterminingLambda	formulaDeterminingLambda
generateGraphs	generateGraphs
getColumn	getColumn
getColumn,PhenList,character-method	PhenList-class
getColumnBatchAdjusted	getColumnBatchAdjusted
getColumnBatchAdjusted,PhenList,character-method	PhenList-class
getColumnView	getColumnView
getColumnView,htestPhenStat-method	htestPhenStat-class
getCountMatrices	getCountMatrices
getCountMatrices,PhenTestResult-method	PhenTestResult-class
getDataset	getDataset
getGenotypeEffect	getGenotypeEffect
getGenotypeEffect,PhenTestResult-method	PhenTestResult-class
getMatrix	getMatrix
getMatrix,htestPhenStat-method	htestPhenStat-class
getPercentageMatrix	getPercentageMatrix
getPercentageMatrix,htestPhenStat-method	htestPhenStat-class
getStat	getStat
getStat,PhenList-method	PhenList-class
getVariable	getVariable
getVariable,PhenTestResult-method	PhenTestResult-class
getVariables	getVariables
getVariables,PhenList-method	PhenList-class
hemiGenotype	hemiGenotype
hemiGenotype,PhenList-method	PhenList-class
htest-class	htest-class
htestPhenStat-class	htestPhenStat-class
LargeDataObject-class	LargeDataObject-class
LRDataset	LRDataset
matrixCount	matrixCount
matrixCount,htestPhenStat-method	htestPhenStat-class
method	method
method,PhenTestResult-method	PhenTestResult-class
methodText	methodText
methodText,PhenTestResult-method	PhenTestResult-class
modelFormula	modelFormula
modelFormulaLR	modelFormulaLR
multipleBatches	multipleBatches
multipleBatches,PhenList-method	PhenList-class
noSexes	noSexes
noSexes,PhenList-method	noSexes
noSexes,PhenTestResult-method	noSexes
parameters	parameters
parameters,PhenTestResult-method	PhenTestResult-class
parserOutputSummary	parserOutputSummary
parserOutputSummaryLR	parserOutputSummaryLR
parserOutputTFSummary	parserOutputTFSummary
PhenList	PhenList
PhenList-class	PhenList-class
PhenTestResult	PhenTestResult
PhenTestResult-class	PhenTestResult-class
plotResidualPredicted	plotResidualPredicted
printHead,LargeDataObject-method	LargeDataObject-class
printLROutput	printLROutput
printTabStyle	printTabStyle
pvalue	pvalue
pvalue,htestPhenStat-method	htestPhenStat-class
qqplotGenotype	qqplotGenotype
qqplotRandomEffects	qqplotRandomEffects
qqplotRotatedResiduals	qqplotRotatedResiduals
recommendMethod	recommendMethod
refGenotype	refGenotype
refGenotype,PhenList-method	PhenList-class
refGenotype,PhenTestResult-method	PhenTestResult-class
reverseTransformValues	reverseTransformValues
RRTest	RRTest
scatterplotGenotypeWeight	scatterplotGenotypeWeight
scatterplotSexGenotypeBatch	scatterplotSexGenotypeBatch
setBatch	setBatch
setBatch,PhenList,character-method	PhenList-class
setGenotype	setGenotype
setGenotype,PhenList,character-method	PhenList-class
setMissingValue	setMissingValue
setMissingValue,PhenList,character-method	PhenList-class
setSex	setSex
setSex,PhenList,character-method	PhenList-class
setWeight	setWeight
setWeight,PhenList,character-method	PhenList-class
show,htestPhenStat-method	htestPhenStat-class
show,LargeDataObject-method	LargeDataObject-class
show,PhenTestResult-method	PhenTestResult-class
startLRModel	startLRModel
startModel	startModel
startTFModel	startTFModel
subsetText	subsetText
subsetText,htestPhenStat-method	htestPhenStat-class
summaryOutput	summaryOutput
testDataset	testDataset
testFinalLRModel	testFinalLRModel
testFinalModel	testFinalModel
testGenotype	testGenotype
testGenotype,PhenList-method	PhenList-class
testGenotype,PhenTestResult-method	PhenTestResult-class
TFDataset	TFDataset
transformation	transformation
transformationText	transformationText
transformationText,PhenTestResult-method	PhenTestResult-class
transformValues	transformValues
vectorOutput	vectorOutput
vectorOutputMatrices	vectorOutputMatrices
weightIn	weightIn
weightIn,PhenList-method	weightIn
weightIn,PhenTestResult-method	weightIn
weightIn-methods	weightIn
