Statistical analysis of phenotypic data

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Documentation for package ‘PhenStat’ version 2.18.0

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A B C D F G H J L M N P Q R S T V W

-- A --

analysedDataset Method "analysedDataset"
analysedDataset-method Class "PhenTestResult"
analysedDatasetPhenList Method "analysedDatasetPhenList"
analysedSubset Method "analysedSubset"
analysisResults Method "analysisResults"
analysisResults-method Class "PhenTestResult"

-- B --

batchIn Method "batchIn"
batchIn-method Method "batchIn"
batchIn-methods Method "batchIn"
boxplotResidualBatch Method "boxplotResidualBatch"
boxplotSexGenotype Method "boxplotSexGenotype"
boxplotSexGenotypeBatch Method "boxplotSexGenotypeBatch"
boxplotSexGenotypeBatchAdjusted Method "boxplotSexGenotypeBatchAdjusted"
boxplotSexGenotypeResult Method "boxplotSexGenotypeResult"
boxplotSexGenotypeWeightBatchAdjusted Method "boxplotSexGenotypeWeightBatchAdjusted"

-- C --

categoricalBarplot Method "categoricalBarplot"
checkDataset Method "checkDataset"
classificationTag Method "classificationTag"
comparison Method "comparison"

-- D --

dataset Method "dataset"
dataset-method Class "PhenList"

-- F --

finalLRModel Method "finalLRModel"
finalModel Method "finalModel"
finalTFModel Method "finalTFModel"
FisherExactTest Method "FisherExactTest"

-- G --

generateGraphs Method "generateGraphs"
getColumn Method "getColumn"
getColumn-method Class "PhenList"
getColumnBatchAdjusted Method "getColumnBatchAdjusted"
getColumnBatchAdjusted-method Class "PhenList"
getColumnView Method "getColumnView"
getColumnWeightBatchAdjusted Method "getColumnWeightBatchAdjusted"
getColumnWeightBatchAdjusted-method Class "PhenList"
getCountMatrices Method "getCountMatrices"
getCountMatrices-method Class "PhenTestResult"
getDataset Method "getDataset"
getGenotypeEffect Method "getGenotypeEffect"
getGenotypeEffect-method Class "PhenTestResult"
getMatrix Method "getMatrix"
getPercentageMatrix Method "getPercentageMatrix"
getStat Method "getStat"
getStat-method Class "PhenList"
getVariable Method "getVariable"
getVariable-method Class "PhenTestResult"
getVariables Method "getVariables"
getVariables-method Class "PhenList"

-- H --

hemiGenotype Method "hemiGenotype"
hemiGenotype-method Class "PhenList"

-- J --

JSONOutput Method "JSONOutput"

-- L --

LRDataset Method "LRDataset"

-- M --

matrixCount Method "matrixCount"
method Method "method"
method-method Class "PhenTestResult"
methodText Method "methodText"
methodText-method Class "PhenTestResult"
multipleBatches Method "multipleBatches"
multipleBatches-method Class "PhenList"

-- N --

noSexes Method "noSexes"
noSexes-method Method "noSexes"

-- P --

parameters Method "parameters"
parameters-method Class "PhenTestResult"
parserOutputSummary Method "parserOutputSummary"
parserOutputSummaryLR Method "parserOutputSummaryLR"
parserOutputTFSummary Method "parserOutputTFSummary"
PhenList Method "PhenList"
PhenList-class Class "PhenList"
PhenStatReport Generating a pdf report from a PhenList object
PhenTestResult Method "PhenTestResult"
PhenTestResult-class Class "PhenTestResult"
plot.PhenList Plot Phenlist object
plot.PhenTestResult Plot phenTestResult object
plotResidualPredicted Method "plotResidualPredicted"
pvalue Method "pvalue"

-- Q --

qqplotGenotype Method "qqplotGenotype"
qqplotRandomEffects Method "qqplotRandomEffects"
qqplotRotatedResiduals Method "qqplotRotatedResiduals"

-- R --

recommendMethod Method "recommendMethod"
refGenotype Method "refGenotype"
refGenotype-method Class "PhenList"
refGenotype-method Class "PhenTestResult"
RRTest Method "RRTest"

-- S --

scatterplotGenotypeWeight Method "scatterplotGenotypeWeight"
scatterplotGenotypeWeightResult Method "scatterplotGenotypeWeightResult"
scatterplotSexGenotypeBatch Method "scatterplotSexGenotypeBatch"
scatterplotSexGenotypeBatchResult Method "scatterplotSexGenotypeBatchResult"
setBatch Method "setBatch"
setBatch-method Class "PhenList"
setGenotype Method "setGenotype"
setGenotype-method Class "PhenList"
setMissingValue Method "setMissingValue"
setMissingValue-method Class "PhenList"
setSex Method "setSex"
setSex-method Class "PhenList"
setWeight Method "setWeight"
setWeight-method Class "PhenList"
show-method Class "PhenTestResult"
startLRModel Method "startLRModel"
startModel Method "startModel"
startTFModel Method "startTFModel"
subsetText Method "subsetText"
summary.PhenTestResult summary
summaryOutput Method "summaryOutput"

-- T --

testDataset Method "testDataset"
testFinalLRModel Method "testFinalLRModel"
testFinalModel Method "testFinalModel"
testGenotype Method "testGenotype"
testGenotype-method Class "PhenList"
testGenotype-method Class "PhenTestResult"
TFDataset Method "TFDataset"
transformation Method "transformation"
transformationJSON Method "transformationJSON"
transformationText Method "transformationText"
transformationText-method Class "PhenTestResult"

-- V --

vectorOutput Method "vectorOutput"
vectorOutputMatrices Method "vectorOutputMatrices"

-- W --

weightIn Method "weightIn"
weightIn-method Method "weightIn"
weightIn-methods Method "weightIn"