Statistical analysis of phenotypic data

---

Documentation for package ‘PhenStat’ version 2.36.0

• 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"