# Statistical analysis of phenotypic data

## Documentation for package ‘PhenStat’ version 2.18.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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"