Package: PhenStat 2.43.0
Hamed Haselimashhadi
PhenStat: Statistical analysis of phenotypic data
Package contains methods for statistical analysis of phenotypic data.
Authors:
PhenStat_2.43.0.tar.gz
PhenStat_2.43.0.zip(r-4.5)PhenStat_2.43.0.zip(r-4.4)PhenStat_2.43.0.zip(r-4.3)
PhenStat_2.43.0.tgz(r-4.4-any)PhenStat_2.43.0.tgz(r-4.3-any)
PhenStat_2.43.0.tar.gz(r-4.5-noble)PhenStat_2.43.0.tar.gz(r-4.4-noble)
PhenStat_2.43.0.tgz(r-4.4-emscripten)PhenStat_2.43.0.tgz(r-4.3-emscripten)
PhenStat.pdf |PhenStat.html✨
PhenStat/json (API)
NEWS
| # Install 'PhenStat' in R: |
| install.packages('PhenStat', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:PhenStat-2.43.0(bioc 3.21)PhenStat-2.42.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 2 months agofrom:59cb12c86c. Checks:OK: 1 NOTE: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 30 2024 |
| R-4.5-win | NOTE | Nov 30 2024 |
| R-4.5-linux | NOTE | Nov 30 2024 |
| R-4.4-win | NOTE | Nov 30 2024 |
| R-4.4-mac | NOTE | Nov 30 2024 |
| R-4.3-win | NOTE | Nov 30 2024 |
| R-4.3-mac | NOTE | Nov 30 2024 |
Exports:analysedDatasetanalysisResultsboxplotSexGenotypecheckDatasetcolumnChecksPhenListPhenStatReportplot.PhenListplot.PhenTestResultqqplotGenotyperecommendMethodsummary.PhenTestResultsummaryOutputtestDatasetvectorOutput
Dependencies:abindbackportsBiocGenericsbitbit64bootbroomcarcarDataclicliprcodetoolscolorspacecorrplotcowplotcpp11crayonDerivdoBydplyrevaluatefansifarverforcatsforeachFormulaformula.toolsgenericsggplot2glmnetgluegraphgtablehavenhighrhmsisobanditeratorsjomoknitrlabelinglatticelifecyclelme4logistfmagrittrMASSMatrixMatrixModelsmgcvmicemicrobenchmarkminqamitmlmodelrmsgpsmunsellnlmenloptrnnetnortestnumDerivoperator.toolsordinalpanpbkrtestpillarpingrpkgconfigplyrprettyunitsprocessxprogresspspurrrquantregR6RColorBrewerRcppRcppArmadilloRcppEigenRcppGSLRcppParallelRcppZigguratreadrreshapeRfastrlangrpartscalesshapeSmoothWinSparseMstringistringrsurvivaltibbletidyrtidyselecttzdbucminfutf8vctrsviridisLitevroomwithrxfunyaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Method "analysedDataset" | analysedDataset |
| Method "analysedDatasetPhenList" | analysedDatasetPhenList |
| Method "analysedSubset" | analysedSubset |
| Method "analysisResults" | analysisResults |
| Method "batchIn" | batchIn batchIn,PhenList-method batchIn,PhenTestResult-method batchIn-methods |
| Method "boxplotResidualBatch" | boxplotResidualBatch |
| Method "boxplotSexGenotype" | boxplotSexGenotype |
| Method "boxplotSexGenotypeBatch" | boxplotSexGenotypeBatch |
| Method "boxplotSexGenotypeBatchAdjusted" | boxplotSexGenotypeBatchAdjusted |
| Method "boxplotSexGenotypeResult" | boxplotSexGenotypeResult |
| Method "boxplotSexGenotypeWeightBatchAdjusted" | boxplotSexGenotypeWeightBatchAdjusted |
| Method "categoricalBarplot" | categoricalBarplot |
| Method "checkDataset" | checkDataset |
| Method "classificationTag" | classificationTag |
| Method "comparison" | comparison |
| Method "dataset" | dataset |
| Method "finalLRModel" | finalLRModel |
| Method "finalModel" | finalModel |
| Method "finalTFModel" | finalTFModel |
| Method "FisherExactTest" | FisherExactTest |
| Method "generateGraphs" | generateGraphs |
| Method "getColumn" | getColumn |
| Method "getColumnBatchAdjusted" | getColumnBatchAdjusted |
| Method "getColumnView" | getColumnView |
| Method "getColumnWeightBatchAdjusted" | getColumnWeightBatchAdjusted |
| Method "getCountMatrices" | getCountMatrices |
| Method "getDataset" | getDataset |
| Method "getGenotypeEffect" | getGenotypeEffect |
| Method "getMatrix" | getMatrix |
| Method "getPercentageMatrix" | getPercentageMatrix |
| Method "getStat" | getStat |
| Method "getVariable" | getVariable |
| Method "getVariables" | getVariables |
| Method "hemiGenotype" | hemiGenotype |
| Method "JSONOutput" | JSONOutput |
| Method "LRDataset" | LRDataset |
| Method "matrixCount" | matrixCount |
| Method "method" | method |
| Method "methodText" | methodText |
| Method "multipleBatches" | multipleBatches |
| Method "noSexes" | noSexes noSexes,PhenList-method noSexes,PhenTestResult-method |
| Method "parameters" | parameters |
| Method "parserOutputSummary" | parserOutputSummary |
| Method "parserOutputSummaryLR" | parserOutputSummaryLR |
| Method "parserOutputTFSummary" | parserOutputTFSummary |
| Method "PhenList" | PhenList |
| Class "PhenList" | dataset,PhenList-method getColumn,PhenList,character-method getColumnBatchAdjusted,PhenList,character-method getColumnWeightBatchAdjusted,PhenList,character-method getStat,PhenList-method getVariables,PhenList-method hemiGenotype,PhenList-method multipleBatches,PhenList-method PhenList-class refGenotype,PhenList-method setBatch,PhenList,character-method setGenotype,PhenList,character-method setMissingValue,PhenList,character-method setSex,PhenList,character-method setWeight,PhenList,character-method testGenotype,PhenList-method |
| Generating a pdf report from a PhenList object | PhenStatReport |
| Method "PhenTestResult" | PhenTestResult |
| Class "PhenTestResult" | analysedDataset,PhenTestResult-method analysisResults,PhenTestResult-method getCountMatrices,PhenTestResult-method getGenotypeEffect,PhenTestResult-method getVariable,PhenTestResult-method method,PhenTestResult-method methodText,PhenTestResult-method parameters,PhenTestResult-method PhenTestResult-class refGenotype,PhenTestResult-method show,PhenTestResult-method testGenotype,PhenTestResult-method transformationText,PhenTestResult-method |
| Plot Phenlist object | plot.PhenList |
| Plot phenTestResult object | plot.PhenTestResult |
| Method "plotResidualPredicted" | plotResidualPredicted |
| Method "pvalue" | pvalue |
| Method "qqplotGenotype" | qqplotGenotype |
| Method "qqplotRandomEffects" | qqplotRandomEffects |
| Method "qqplotRotatedResiduals" | qqplotRotatedResiduals |
| Method "recommendMethod" | recommendMethod |
| Method "refGenotype" | refGenotype |
| Method "RRTest" | RRTest |
| Method "scatterplotGenotypeWeight" | scatterplotGenotypeWeight |
| Method "scatterplotGenotypeWeightResult" | scatterplotGenotypeWeightResult |
| Method "scatterplotSexGenotypeBatch" | scatterplotSexGenotypeBatch |
| Method "scatterplotSexGenotypeBatchResult" | scatterplotSexGenotypeBatchResult |
| Method "setBatch" | setBatch |
| Method "setGenotype" | setGenotype |
| Method "setMissingValue" | setMissingValue |
| Method "setSex" | setSex |
| Method "setWeight" | setWeight |
| Method "startLRModel" | startLRModel |
| Method "startModel" | startModel |
| Method "startTFModel" | startTFModel |
| Method "subsetText" | subsetText |
| summary | summary.PhenTestResult |
| Method "summaryOutput" | summaryOutput |
| Method "testDataset" | testDataset |
| Method "testFinalLRModel" | testFinalLRModel |
| Method "testFinalModel" | testFinalModel |
| Method "testGenotype" | testGenotype |
| Method "TFDataset" | TFDataset |
| Method "transformation" | transformation |
| Method "transformationJSON" | transformationJSON |
| Method "transformationText" | transformationText |
| Method "vectorOutput" | vectorOutput |
| Method "vectorOutputMatrices" | vectorOutputMatrices |
| Method "weightIn" | weightIn weightIn,PhenList-method weightIn,PhenTestResult-method weightIn-methods |
