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PhenStat (version 2.2.0)

Statistical analysis of phenotypic data

Description

Package contains methods for statistical analysis of phenotypic data such as Mixed Models and Fisher Exact Test.

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Version

Version

2.2.0

License

file LICENSE

Maintainer

Natasha Karp

Last Published

February 15th, 2017

Functions in PhenStat (2.2.0)

getMatrix

Method "getMatrix"
batchIn

Method "batchIn"
analysisResults

Method "analysisResults"
FisherExactTest

Method "FisherExactTest"
finalTFModel

Method "finalTFModel"
getColumn

Method "getColumn"
classificationTag

Method "classificationTag"
columnChecks

Method "columnChecks"
getPercentageMatrix

Method "getPercentageMatrix"
method

Method "method"
modelFormula

Method "modelFormula"
methodText

Method "methodText"
matrixCount

Method "matrixCount"
qqplotRandomEffects

Method "qqplotRandomEffects"
qqplotRotatedResiduals

Method "qqplotRotatedResiduals"
scatterplotGenotypeWeight

Method "scatterplotGenotypeWeight"
scatterplotSexGenotypeBatch

Method "scatterplotSexGenotypeBatch"
vectorOutput

Method "vectorOutput"
vectorOutputMatrices

Method "vectorOutputMatrices"
getColumnBatchAdjusted

Method "getColumnBatchAdjusted"
getStat

Method "getStat"
printLROutput

Method "printLROutput"
getVariable

Method "getVariable"
recommendMethod

Method "recommendMethod"
testDataset

Method "testDataset"
refGenotype

Method "refGenotype"
printTabStyle

Method "printTabStyle"
testFinalLRModel

Method "testFinalLRModel"
categoricalBarplot

Method "categoricalBarplot"
checkDataset

Method "checkDataset"
comparison

Method "comparison"
getColumnView

Method "getColumnView"
columnLevels

Method "columnLevels"
getCountMatrices

Method "getCountMatrices"
htest-class

Class "htest"
htestPhenStat-class

Class "htestPhenStat"
noSexes

Method "noSexes"
parameters

Method "parameters"
setWeight

Method "setWeight"
startLRModel

Method "startLRModel"
transformation

Method "transformation"
TFDataset

Method "TFDataset"
boxplotSexGenotype

Method "boxplotSexGenotype"
boxplotResidualBatch

Method "boxplotResidualBatch"
dim

Method "dim"
dataset

Method "dataset"
LargeDataObject-class

Class "LargeDataObject"
parserOutputTFSummary

Method "parserOutputTFSummary"
LRDataset

Method "LRDataset"
PhenList

Method "PhenList"
PhenTestResult-class

Class "PhenTestResult"
PhenList-class

Class "PhenList"
setBatch

Method "setBatch"
setGenotype

Method "setGenotype"
startModel

Method "startModel"
startTFModel

Method "startTFModel"
finalLRModel

Method "finalLRModel"
boxplotSexGenotypeBatchAdjusted

Method "boxplotSexGenotypeBatchAdjusted"
boxplotSexGenotypeBatch

Method "boxplotSexGenotypeBatch"
finalModel

Method "finalModel"
formulaDeterminingLambda

Method "formulaDeterminingLambda"
generateGraphs

Method "generateGraphs"
getVariables

Method "getVariables"
hemiGenotype

Method "hemiGenotype"
parserOutputSummary

Method "parserOutputSummary"
parserOutputSummaryLR

Method "parserOutputSummaryLR"
pvalue

Method "pvalue"
qqplotGenotype

Method "qqplotGenotype"
reverseTransformValues

Method "reverseTransformValues"
RRTest

Method "RRTest"
testFinalModel

Method "testFinalModel"
testGenotype

Method "testGenotype"
weightIn

Method "weightIn"
analysedDataset

Method "analysedDataset"
getDataset

Method "getDataset"
getGenotypeEffect

Method "getGenotypeEffect"
analysedSubset

Method "analysedSubset"
modelFormulaLR

Method "modelFormulaLR"
multipleBatches

Method "multipleBatches"
plotResidualPredicted

Method "plotResidualPredicted"
PhenTestResult

Method "PhenTestResult"
setMissingValue

Method "setMissingValue"
setSex

Method "setSex"
subsetText

Method "subsetText"
summaryOutput

Method "summaryOutput"
transformationText

Method "transformationText"
transformValues

Method "transformValues"