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PhenStat (version 2.6.0)

Statistical analysis of phenotypic data

Description

Package contains methods for statistical analysis of phenotypic data.

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Version

Version

2.6.0

License

file LICENSE

Maintainer

Last Published

February 15th, 2017

Functions in PhenStat (2.6.0)

Method "checkDataset"

boxplotSexGenotypeBatch

Method "boxplotSexGenotypeBatch"

Method "RRTest"

Method "getStat"

analysedDatasetPhenList

Method "analysedDatasetPhenList"

multipleBatches

Method "multipleBatches"

FisherExactTest

Method "FisherExactTest"

Method "JSONOutput"

Class "PhenList"

Method "finalModel"

Method "PhenList"

Method "TFDataset"

getColumnBatchAdjusted

Method "getColumnBatchAdjusted"

classificationTag

Method "classificationTag"

htestPhenStat-class

Class "htestPhenStat"

formulaDeterminingLambda

Method "formulaDeterminingLambda"

boxplotResidualBatch

Method "boxplotResidualBatch"

boxplotSexGenotypeResult

Method "boxplotSexGenotypeResult"

boxplotSexGenotype

Method "boxplotSexGenotype"

Method "modelFormula"

Method "summaryOutput"

boxplotSexGenotypeBatchAdjusted

Method "boxplotSexGenotypeBatchAdjusted"

scatterplotGenotypeWeightResult

Method "scatterplotGenotypeWeightResult"

plotResidualPredicted

Method "plotResidualPredicted"

Method "finalLRModel"

Method "setSex"

categoricalBarplot

Method "categoricalBarplot"

analysisResults

Method "analysisResults"

vectorOutputMatrices

Method "vectorOutputMatrices"

getColumnWeightBatchAdjusted

Method "getColumnWeightBatchAdjusted"

Method "PhenTestResult"

boxplotSexGenotypeWeightBatchAdjusted

Method "boxplotSexGenotypeWeightBatchAdjusted"

Method "methodText"

Method "noSexes"

determiningLambda

Method "determiningLambda"

parserOutputSummary

Method "parserOutputSummary"

Method "LRDataset"

Method "batchIn"

getGenotypeEffect

Method "getGenotypeEffect"

testFinalLRModel

Method "testFinalLRModel"

parserOutputSummaryLR

Method "parserOutputSummaryLR"

analysedDataset

Method "analysedDataset"

parserOutputTFSummary

Method "parserOutputTFSummary"

Method "getVariable"

Method "parameters"

Method "columnLevels"

transformationText

Method "transformationText"

performTransformation

Method "performTransformation"

Method "getColumnView"

Method "qqplotGenotype"

Method "matrixCount"

Method "modelFormulaLR"

Method "testFinalModel"

Method "getDataset"

Method "vectorOutput"

Method "getVariables"

Method "setWeight"

Method "startModel"

Method "testDataset"

qqplotRandomEffects

Method "qqplotRandomEffects"

transformationJSON

Method "transformationJSON"

Method "startLRModel"

Method "weightIn"

Method "subsetText"

getCountMatrices

Method "getCountMatrices"

Method "columnChecks"

performReverseTransformation

Method "performReverseTransformation"

scatterplotGenotypeWeight

Method "scatterplotGenotypeWeight"

Method "setBatch"

PhenTestResult-class

Class "PhenTestResult"

Method "method"

Method "hemiGenotype"

Method "getColumn"

qqplotRotatedResiduals

Method "qqplotRotatedResiduals"

recommendMethod

Method "recommendMethod"

Method "testGenotype"

LargeDataObject-class

Class "LargeDataObject"

Method "analysedSubset"

Method "dataset"

getPercentageMatrix

Method "getPercentageMatrix"

Method "pvalue"

Method "printLROutput"

Method "finalTFModel"

Method "printTabStyle"

scatterplotSexGenotypeBatchResult

Method "scatterplotSexGenotypeBatchResult"

setMissingValue

Method "setMissingValue"

Method "generateGraphs"

Method "getMatrix"

Method "comparison"

Method "transformation"

scatterplotSexGenotypeBatch

Method "scatterplotSexGenotypeBatch"

Method "startTFModel"

Method "refGenotype"

Method "setGenotype"