PhenStat: Statistical analysis of phenotypic data

Package contains methods for statistical analysis of phenotypic data.

AuthorNatalja Kurbatova, Natasha Karp, Jeremy Mason
Date of publicationNone
MaintainerJeremy Mason <jmason@ebi.ac.uk>
Licensefile LICENSE
Version2.8.0

View on Bioconductor

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

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

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.