PhenStat: Statistical analysis of phenotypic data

Share:

Package contains methods for statistical analysis of phenotypic data.

Author
Natalja Kurbatova, Natasha Karp, Jeremy Mason
Date of publication
None
Maintainer
Jeremy Mason <jmason@ebi.ac.uk>
License
file LICENSE
Version
2.8.0

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"

Files in this package

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