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PhenStat (version 2.4.0)

Statistical analysis of phenotypic data

Description

Package contains methods for statistical analysis of phenotypic data.

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Version

Version

2.4.0

License

file LICENSE

Maintainer

Natasha Karp

Last Published

February 15th, 2017

Functions in PhenStat (2.4.0)

analysisResults

Method "analysisResults"

multipleBatches

Method "multipleBatches"

Method "noSexes"

plotResidualPredicted

Method "plotResidualPredicted"

setMissingValue

Method "setMissingValue"

Method "setSex"

Method "printLROutput"

testFinalLRModel

Method "testFinalLRModel"

Method "testDataset"

Method "analysedSubset"

classificationTag

Method "classificationTag"

Method "getMatrix"

Method "checkDataset"

formulaDeterminingLambda

Method "formulaDeterminingLambda"

FisherExactTest

Method "FisherExactTest"

getPercentageMatrix

Method "getPercentageMatrix"

Method "comparison"

Method "dataset"

getColumnWeightBatchAdjusted

Method "getColumnWeightBatchAdjusted"

getCountMatrices

Method "getCountMatrices"

Method "LRDataset"

Method "matrixCount"

htestPhenStat-class

Class "htestPhenStat"

Class "PhenList"

Method "PhenList"

Method "refGenotype"

Method "RRTest"

Method "TFDataset"

Method "transformation"

boxplotSexGenotypeBatchAdjusted

Method "boxplotSexGenotypeBatchAdjusted"

boxplotSexGenotypeResult

Method "boxplotSexGenotypeResult"

boxplotSexGenotypeWeightBatchAdjusted

Method "boxplotSexGenotypeWeightBatchAdjusted"

categoricalBarplot

Method "categoricalBarplot"

boxplotSexGenotype

Method "boxplotSexGenotype"

boxplotSexGenotypeBatch

Method "boxplotSexGenotypeBatch"

getColumnBatchAdjusted

Method "getColumnBatchAdjusted"

Method "getColumnView"

PhenTestResult-class

Class "PhenTestResult"

qqplotRotatedResiduals

Method "qqplotRotatedResiduals"

Method "PhenTestResult"

recommendMethod

Method "recommendMethod"

scatterplotSexGenotypeBatch

Method "scatterplotSexGenotypeBatch"

Method "finalModel"

Method "finalTFModel"

Method "getVariables"

Method "JSONOutput"

Method "hemiGenotype"

LargeDataObject-class

Class "LargeDataObject"

Method "parameters"

parserOutputSummary

Method "parserOutputSummary"

Method "setBatch"

Method "testFinalModel"

Method "setGenotype"

Method "testGenotype"

Method "weightIn"

Method "batchIn"

boxplotResidualBatch

Method "boxplotResidualBatch"

Method "finalLRModel"

scatterplotSexGenotypeBatchResult

Method "scatterplotSexGenotypeBatchResult"

Method "startModel"

Method "startTFModel"

vectorOutputMatrices

Method "vectorOutputMatrices"

Method "vectorOutput"

Method "generateGraphs"

Method "getColumn"

Method "getDataset"

getGenotypeEffect

Method "getGenotypeEffect"

Method "method"

Method "methodText"

performTransformation

Method "performTransformation"

Method "qqplotGenotype"

qqplotRandomEffects

Method "qqplotRandomEffects"

transformationJSON

Method "transformationJSON"

Method "startLRModel"

Method "setWeight"

performReverseTransformation

Method "performReverseTransformation"

transformationText

Method "transformationText"

analysedDataset

Method "analysedDataset"

Method "columnChecks"

analysedDatasetPhenList

Method "analysedDatasetPhenList"

Method "getStat"

Method "columnLevels"

Method "getVariable"

Method "modelFormula"

parserOutputSummaryLR

Method "parserOutputSummaryLR"

Method "modelFormulaLR"

parserOutputTFSummary

Method "parserOutputTFSummary"

Method "printTabStyle"

Method "pvalue"

scatterplotGenotypeWeight

Method "scatterplotGenotypeWeight"

scatterplotGenotypeWeightResult

Method "scatterplotGenotypeWeightResult"

Method "subsetText"

Method "summaryOutput"