Man pages for PhenStat
Statistical analysis of phenotypic data
| 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" |
| 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" |
| 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" |
| summaryPhenListResult | summary |
| 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" |
