PhenStat: Statistical analysis of phenotypic data
Version 2.10.0

Package contains methods for statistical analysis of phenotypic data.

Browse man pages Browse package API and functions Browse package files

AuthorNatalja Kurbatova, Natasha Karp, Jeremy Mason
Date of publicationNone
MaintainerJeremy Mason <jmason@ebi.ac.uk>
Licensefile LICENSE
Version2.10.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("PhenStat")

Man pages

analysedDataset: Method "analysedDataset"
analysedDatasetPhenList: Method "analysedDatasetPhenList"
analysedSubset: Method "analysedSubset"
analysisResults: Method "analysisResults"
batchIn: Method "batchIn"
boxplotResidualBatch: Method "boxplotResidualBatch"
boxplotSexGenotype: Method "boxplotSexGenotype"
boxplotSexGenotypeBatch: Method "boxplotSexGenotypeBatch"
boxplotSexGenotypeBatchAdjusted: Method "boxplotSexGenotypeBatchAdjusted"
boxplotSexGenotypeResult: Method "boxplotSexGenotypeResult"
boxplotSexGenotypeWeightBatchAdjusted: Method "boxplotSexGenotypeWeightBatchAdjusted"
categoricalBarplot: Method "categoricalBarplot"
checkDataset: Method "checkDataset"
classificationTag: Method "classificationTag"
columnChecks: Method "columnChecks"
columnLevels: Method "columnLevels"
comparison: Method "comparison"
dataset: Method "dataset"
determiningLambda: Method "determiningLambda"
dim: Method "dim"
finalLRModel: Method "finalLRModel"
finalModel: Method "finalModel"
finalTFModel: Method "finalTFModel"
FisherExactTest: Method "FisherExactTest"
formulaDeterminingLambda: Method "formulaDeterminingLambda"
generateGraphs: Method "generateGraphs"
getColumn: Method "getColumn"
getColumnBatchAdjusted: Method "getColumnBatchAdjusted"
getColumnView: Method "getColumnView"
getColumnWeightBatchAdjusted: Method "getColumnWeightBatchAdjusted"
getCountMatrices: Method "getCountMatrices"
getDataset: Method "getDataset"
getGenotypeEffect: Method "getGenotypeEffect"
getMatrix: Method "getMatrix"
getPercentageMatrix: Method "getPercentageMatrix"
getStat: Method "getStat"
getVariable: Method "getVariable"
getVariables: Method "getVariables"
hemiGenotype: Method "hemiGenotype"
htest-class: Class "htest"
htestPhenStat-class: Class "htestPhenStat"
JSONOutput: Method "JSONOutput"
LargeDataObject-class: Class "LargeDataObject"
LRDataset: Method "LRDataset"
matrixCount: Method "matrixCount"
method: Method "method"
methodText: Method "methodText"
modelFormula: Method "modelFormula"
modelFormulaLR: Method "modelFormulaLR"
multipleBatches: Method "multipleBatches"
noSexes: Method "noSexes"
parameters: Method "parameters"
parserOutputSummary: Method "parserOutputSummary"
parserOutputSummaryLR: Method "parserOutputSummaryLR"
parserOutputTFSummary: Method "parserOutputTFSummary"
performReverseTransformation: Method "performReverseTransformation"
performTransformation: Method "performTransformation"
PhenList: Method "PhenList"
PhenList-class: Class "PhenList"
PhenTestResult: Method "PhenTestResult"
PhenTestResult-class: Class "PhenTestResult"
plotResidualPredicted: Method "plotResidualPredicted"
printLROutput: Method "printLROutput"
printTabStyle: Method "printTabStyle"
pvalue: Method "pvalue"
qqplotGenotype: Method "qqplotGenotype"
qqplotRandomEffects: Method "qqplotRandomEffects"
qqplotRotatedResiduals: Method "qqplotRotatedResiduals"
recommendMethod: Method "recommendMethod"
refGenotype: Method "refGenotype"
RRTest: Method "RRTest"
scatterplotGenotypeWeight: Method "scatterplotGenotypeWeight"
scatterplotGenotypeWeightResult: Method "scatterplotGenotypeWeightResult"
scatterplotSexGenotypeBatch: Method "scatterplotSexGenotypeBatch"
scatterplotSexGenotypeBatchResult: Method "scatterplotSexGenotypeBatchResult"
setBatch: Method "setBatch"
setGenotype: Method "setGenotype"
setMissingValue: Method "setMissingValue"
setSex: Method "setSex"
setWeight: Method "setWeight"
startLRModel: Method "startLRModel"
startModel: Method "startModel"
startTFModel: Method "startTFModel"
subsetText: Method "subsetText"
summaryOutput: Method "summaryOutput"
testDataset: Method "testDataset"
testFinalLRModel: Method "testFinalLRModel"
testFinalModel: Method "testFinalModel"
testGenotype: Method "testGenotype"
TFDataset: Method "TFDataset"
transformation: Method "transformation"
transformationJSON: Method "transformationJSON"
transformationText: Method "transformationText"
vectorOutput: Method "vectorOutput"
vectorOutputMatrices: Method "vectorOutputMatrices"
weightIn: Method "weightIn"

Functions

FisherExactTest Man page Source code
JSONOutput Man page Source code
LRDataset Man page Source code
LargeDataObject-class Man page
PhenList Man page Source code
PhenList-class Man page
PhenTestResult Man page Source code
PhenTestResult-class Man page
RRTest Man page Source code
TFDataset Man page Source code
analysedDataset Man page Source code
analysedDataset,PhenTestResult-method Man page
analysedDatasetPhenList Man page Source code
analysedSubset Man page Source code
analysedSubset,htestPhenStat-method Man page
analysisResults Man page Source code
analysisResults,PhenTestResult-method Man page
batchIn Man page
batchIn,PhenList-method Man page
batchIn,PhenTestResult-method Man page
batchIn-methods Man page
boxplotResidualBatch Man page Source code
boxplotSexGenotype Man page Source code
boxplotSexGenotypeBatch Man page Source code
boxplotSexGenotypeBatchAdjusted Man page Source code
boxplotSexGenotypeResult Man page Source code
boxplotSexGenotypeWeightBatchAdjusted Man page Source code
categoricalBarplot Man page Source code
checkDataset Man page Source code
classificationTag Man page Source code
columnChecks Man page Source code
columnLevels Man page Source code
comparison Man page Source code
comparison,htestPhenStat-method Man page
dataset Man page
dataset,PhenList-method Man page
determiningLambda Man page Source code
dim.PhenList Man page Source code
finalLRModel Man page Source code
finalModel Man page Source code
finalTFModel Man page Source code
formulaDeterminingLambda Man page Source code
generateGraphs Man page Source code
getColumn Man page
getColumn,PhenList,character-method Man page
getColumnBatchAdjusted Man page
getColumnBatchAdjusted,PhenList,character-method Man page
getColumnView Man page
getColumnView,htestPhenStat-method Man page
getColumnWeightBatchAdjusted Man page
getColumnWeightBatchAdjusted,PhenList,character-method Man page
getCountMatrices Man page
getCountMatrices,PhenTestResult-method Man page
getDataset Man page Source code
getGenotypeEffect Man page
getGenotypeEffect,PhenTestResult-method Man page
getMatrix Man page
getMatrix,htestPhenStat-method Man page
getPercentageMatrix Man page
getPercentageMatrix,htestPhenStat-method Man page
getStat Man page
getStat,PhenList-method Man page
getVariable Man page Source code
getVariable,PhenTestResult-method Man page
getVariables Man page
getVariables,PhenList-method Man page
hemiGenotype Man page Source code
hemiGenotype,PhenList-method Man page
htest-class Man page
htestPhenStat-class Man page
matrixCount Man page Source code
matrixCount,htestPhenStat-method Man page
method Man page Source code
method,PhenTestResult-method Man page
methodText Man page Source code
methodText,PhenTestResult-method Man page
modelFormula Man page Source code
modelFormulaLR Man page Source code
multipleBatches Man page
multipleBatches,PhenList-method Man page
noSexes Man page
noSexes,PhenList-method Man page
noSexes,PhenTestResult-method Man page
parameters Man page Source code
parameters,PhenTestResult-method Man page
parserOutputSummary Man page Source code
parserOutputSummaryLR Man page Source code
parserOutputTFSummary Man page Source code
performReverseTransformation Man page Source code
performTransformation Man page Source code
plotResidualPredicted Man page Source code
printHead,LargeDataObject-method Man page
printLROutput Man page Source code
printTabStyle Man page Source code
pvalue Man page Source code
pvalue,htestPhenStat-method Man page
qqplotGenotype Man page Source code
qqplotRandomEffects Man page Source code
qqplotRotatedResiduals Man page Source code
recommendMethod Man page Source code
refGenotype Man page Source code Source code
refGenotype,PhenList-method Man page
refGenotype,PhenTestResult-method Man page
scatterplotGenotypeWeight Man page Source code
scatterplotGenotypeWeightResult Man page Source code
scatterplotSexGenotypeBatch Man page Source code
scatterplotSexGenotypeBatchResult Man page Source code
setBatch Man page
setBatch,PhenList,character-method Man page
setGenotype Man page
setGenotype,PhenList,character-method Man page
setMissingValue Man page
setMissingValue,PhenList,character-method Man page
setSex Man page
setSex,PhenList,character-method Man page
setWeight Man page
setWeight,PhenList,character-method Man page
show,LargeDataObject-method Man page
show,PhenTestResult-method Man page
show,htestPhenStat-method Man page
startLRModel Man page Source code
startModel Man page Source code
startTFModel Man page Source code
subsetText Man page Source code
subsetText,htestPhenStat-method Man page Man page
summaryOutput Man page Source code
testDataset Man page Source code
testFinalLRModel Man page Source code
testFinalModel Man page Source code
testGenotype Man page Source code Source code
testGenotype,PhenList-method Man page
testGenotype,PhenTestResult-method Man page
transformation Man page Source code
transformationJSON Man page Source code
transformationText Man page Source code
transformationText,PhenTestResult-method Man page
vectorOutput Man page Source code
vectorOutputMatrices Man page Source code
weightIn Man page
weightIn,PhenList-method Man page
weightIn,PhenTestResult-method Man page
weightIn-methods Man page

Files

DESCRIPTION
LICENSE
NAMESPACE
NOTICE
R
R/FETFramework.R
R/JSONOutput.R
R/LogisticFramework.R
R/MMFramework.R
R/PhenList.R
R/PhenTestResult.R
R/RRFramework.R
R/TFFramework.R
R/classes.R
R/classification.R
R/diagnostictest.R
R/graphsDataset.R
R/graphsResults.R
R/summaryOutput.R
R/testDataset.R
R/transformation.R
R/vectorOutput.R
build
build/vignette.rds
inst
inst/NEWS.Rd
inst/doc
inst/doc/PhenStat.R
inst/doc/PhenStat.Rnw
inst/doc/PhenStat.pdf
inst/doc/PhenStatUsersGuide.pdf
inst/extdata
inst/extdata/Tox3CaDataset.csv
inst/extdata/permutationTest.csv
inst/extdata/test1.csv
inst/extdata/test1_1sex.csv
inst/extdata/test2.csv
inst/extdata/test3.csv
inst/extdata/test4.csv
inst/extdata/test5.csv
inst/extdata/test6_RR.csv
inst/extdata/test7_TFE.csv
inst/extdata/testLR.csv
inst/extdata/test_Akt2.csv
inst/extdata/test_categorical.csv
inst/extdata/test_categorical_normal.csv
inst/extdata/test_jitter.csv
inst/unitTests
inst/unitTests/unitTests.R
man
man/FisherExactTest.Rd
man/JSONOutput.Rd
man/LRDataset.Rd
man/LargeDataObject-class.Rd
man/PhenList-class.Rd
man/PhenList.Rd
man/PhenTestResult-class.Rd
man/PhenTestResult.Rd
man/RRTest.Rd
man/TFDataset.Rd
man/analysedDataset.Rd
man/analysedDatasetPhenList.Rd
man/analysedSubset.Rd
man/analysisResults.Rd
man/batchIn.Rd
man/boxplotResidualBatch.Rd
man/boxplotSexGenotype.Rd
man/boxplotSexGenotypeBatch.Rd
man/boxplotSexGenotypeBatchAdjusted.Rd
man/boxplotSexGenotypeResult.Rd
man/boxplotSexGenotypeWeightBatchAdjusted.Rd
man/categoricalBarplot.Rd
man/checkDataset.Rd
man/classificationTag.Rd
man/columnChecks.Rd
man/columnLevels.Rd
man/comparison.Rd
man/dataset.Rd
man/determiningLambda.Rd
man/dim.Rd
man/finalLRModel.Rd
man/finalModel.Rd
man/finalTFModel.Rd
man/formulaDeterminingLambda.Rd
man/generateGraphs.Rd
man/getColumn.Rd
man/getColumnBatchAdjusted.Rd
man/getColumnView.Rd
man/getColumnWeightBatchAdjusted.Rd
man/getCountMatrices.Rd
man/getDataset.Rd
man/getGenotypeEffect.Rd
man/getMatrix.Rd
man/getPercentageMatrix.Rd
man/getStat.Rd
man/getVariable.Rd
man/getVariables.Rd
man/hemiGenotype.Rd
man/htest-class.Rd
man/htestPhenStat-class.Rd
man/matrixCount.Rd
man/method.Rd
man/methodText.Rd
man/modelFormula.Rd
man/modelFormulaLR.Rd
man/multipleBatches.Rd
man/noSexes.Rd
man/parameters.Rd
man/parserOutputSummary.Rd
man/parserOutputSummaryLR.Rd
man/parserOutputTFSummary.Rd
man/performReverseTransformation.Rd
man/performTransformation.Rd
man/plotResidualPredicted.Rd
man/printLROutput.Rd
man/printTabStyle.Rd
man/pvalue.Rd
man/qqplotGenotype.Rd
man/qqplotRandomEffects.Rd
man/qqplotRotatedResiduals.Rd
man/recommendMethod.Rd
man/refGenotype.Rd
man/scatterplotGenotypeWeight.Rd
man/scatterplotGenotypeWeightResult.Rd
man/scatterplotSexGenotypeBatch.Rd
man/scatterplotSexGenotypeBatchResult.Rd
man/setBatch.Rd
man/setGenotype.Rd
man/setMissingValue.Rd
man/setSex.Rd
man/setWeight.Rd
man/startLRModel.Rd
man/startModel.Rd
man/startTFModel.Rd
man/subsetText.Rd
man/summaryOutput.Rd
man/testDataset.Rd
man/testFinalLRModel.Rd
man/testFinalModel.Rd
man/testGenotype.Rd
man/transformation.Rd
man/transformationJSON.Rd
man/transformationText.Rd
man/vectorOutput.Rd
man/vectorOutputMatrices.Rd
man/weightIn.Rd
tests
tests/runTests.R
vignettes
vignettes/PhenStat.Rnw
PhenStat documentation built on May 20, 2017, 10:56 p.m.