FisherExactTest         Method "FisherExactTest"
JSONOutput              Method "JSONOutput"
LRDataset               Method "LRDataset"
PhenList                Method "PhenList"
PhenList-class          Class "PhenList"
PhenSmoothWin           Complementary function for "testDataset" that
                        allows soft windowing
PhenStatReport          Generating a pdf report from a PhenList object
PhenTestResult          Method "PhenTestResult"
PhenTestResult-class    Class "PhenTestResult"
RRTest                  Method "RRTest"
TFDataset               Method "TFDataset"
analysedDataset         Method "analysedDataset"
analysedDatasetPhenList
                        Method "analysedDatasetPhenList"
analysedSubset          Method "analysedSubset"
analysisResults         Method "analysisResults"
batchIn                 Method "batchIn"
boxplotResidualBatch    Method "boxplotResidualBatch"
boxplotSexGenotype      Method "boxplotSexGenotype"
boxplotSexGenotypeBatch
                        Method "boxplotSexGenotypeBatch"
boxplotSexGenotypeBatchAdjusted
                        Method "boxplotSexGenotypeBatchAdjusted"
boxplotSexGenotypeResult
                        Method "boxplotSexGenotypeResult"
boxplotSexGenotypeWeightBatchAdjusted
                        Method "boxplotSexGenotypeWeightBatchAdjusted"
categoricalBarplot      Method "categoricalBarplot"
checkDataset            Method "checkDataset"
classificationTag       Method "classificationTag"
comparison              Method "comparison"
dataset                 Method "dataset"
finalLRModel            Method "finalLRModel"
finalModel              Method "finalModel"
finalTFModel            Method "finalTFModel"
generateGraphs          Method "generateGraphs"
getColumn               Method "getColumn"
getColumnBatchAdjusted
                        Method "getColumnBatchAdjusted"
getColumnView           Method "getColumnView"
getColumnWeightBatchAdjusted
                        Method "getColumnWeightBatchAdjusted"
getCountMatrices        Method "getCountMatrices"
getDataset              Method "getDataset"
getGenotypeEffect       Method "getGenotypeEffect"
getMatrix               Method "getMatrix"
getPercentageMatrix     Method "getPercentageMatrix"
getStat                 Method "getStat"
getVariable             Method "getVariable"
getVariables            Method "getVariables"
hemiGenotype            Method "hemiGenotype"
matrixCount             Method "matrixCount"
method                  Method "method"
methodText              Method "methodText"
multipleBatches         Method "multipleBatches"
noSexes                 Method "noSexes"
parameters              Method "parameters"
parserOutputSummary     Method "parserOutputSummary"
parserOutputSummaryLR   Method "parserOutputSummaryLR"
parserOutputTFSummary   Method "parserOutputTFSummary"
plot.PhenList           Plot Phenlist object
plot.PhenTestResult     Plot phenTestResult object
plotResidualPredicted   Method "plotResidualPredicted"
pvalue                  Method "pvalue"
qqplotGenotype          Method "qqplotGenotype"
qqplotRandomEffects     Method "qqplotRandomEffects"
qqplotRotatedResiduals
                        Method "qqplotRotatedResiduals"
recommendMethod         Method "recommendMethod"
refGenotype             Method "refGenotype"
scatterplotGenotypeWeight
                        Method "scatterplotGenotypeWeight"
scatterplotGenotypeWeightResult
                        Method "scatterplotGenotypeWeightResult"
scatterplotSexGenotypeBatch
                        Method "scatterplotSexGenotypeBatch"
scatterplotSexGenotypeBatchResult
                        Method "scatterplotSexGenotypeBatchResult"
setBatch                Method "setBatch"
setGenotype             Method "setGenotype"
setMissingValue         Method "setMissingValue"
setSex                  Method "setSex"
setWeight               Method "setWeight"
startLRModel            Method "startLRModel"
startModel              Method "startModel"
startTFModel            Method "startTFModel"
subsetText              Method "subsetText"
summary.PhenTestResult
                        summary
summaryOutput           Method "summaryOutput"
testDataset             Method "testDataset"
testFinalLRModel        Method "testFinalLRModel"
testFinalModel          Method "testFinalModel"
testGenotype            Method "testGenotype"
transformation          Method "transformation"
transformationJSON      Method "transformationJSON"
transformationText      Method "transformationText"
vectorOutput            Method "vectorOutput"
vectorOutputMatrices    Method "vectorOutputMatrices"
weightIn                Method "weightIn"
