API for NormalyzerDE
Evaluation of normalization methods and calculation of differential expression analysis statistics
| Global functions | |
|---|---|
| NormalyzerDataset | Man page Source code |
| NormalyzerEvaluationResults | Man page |
| NormalyzerResults | Man page Source code |
| NormalyzerStatistics | Man page Source code |
| analyzeNormalizations | Man page Source code |
| calculateANOVAPValues | Man page Source code |
| calculateAvgMadMem | Man page Source code |
| calculateAvgReplicateVariation | Man page Source code |
| calculateContrasts | Man page |
| calculateContrasts,NormalyzerStatistics-method | Man page |
| calculateCorrSum | Man page Source code |
| calculateFeatureCV | Man page Source code |
| calculateLimmaContrast | Source code |
| calculatePercentageAvgDiffInMat | Man page Source code |
| calculateReplicateCV | Man page Source code |
| calculateSummarizedCorrelationVector | Man page Source code |
| calculateWelch | Source code |
| createDirectory | Man page Source code |
| detectSingleReplicate | Man page |
| detectSingleReplicate,NormalyzerDataset-method | Man page |
| detectSingletonSample | Man page |
| detectSingletonSample,NormalyzerDataset-method | Man page |
| drawRectangles | Source code |
| elapsedSecondsBetweenSystimes | Man page Source code |
| example_data | Man page |
| example_data_only_values | Man page |
| example_design | Man page |
| example_stat_data | Man page |
| example_stat_summarized_experiment | Man page |
| example_summarized_experiment | Man page |
| example_wide_data | Man page |
| example_wide_design | Man page |
| filterLowRep | Man page Source code |
| filterOnlyNARows | Source code |
| findLowlyVariableFeaturesCVs | Man page Source code |
| generateAnnotatedMatrix | Man page Source code |
| generatePlots | Man page Source code |
| generateStatsReport | Man page Source code |
| getCombinedMatrix | Man page Source code |
| getIndexList | Man page Source code |
| getLowCountSampleFiltered | Man page Source code |
| getRTColumn | Source code |
| getRTNormalizedMatrix | Man page Source code |
| getReplicateSortedData | Man page Source code |
| getRowNAFilterContrast | Man page Source code |
| getSigs | Source code |
| getSmoothedRTNormalizedMatrix | Man page Source code |
| getVerifiedNormalyzerObject | Man page Source code |
| getWidenedRTRange | Man page Source code |
| globalIntensityNormalization | Man page Source code |
| loadData | Man page Source code |
| loadDesign | Man page Source code |
| loadRawDataFromFile | Man page Source code |
| maxQuantToNormalyzer | Source code |
| meanNormalization | Man page Source code |
| medianNormalization | Man page Source code |
| normMethods | Man page Source code |
| normalyzer | Man page Source code |
| normalyzerDE | Man page Source code |
| performCyclicLoessNormalization | Man page Source code |
| performGlobalRLRNormalization | Man page Source code |
| performNoNormalization | Man page Source code |
| performNormalizations | Man page |
| performNormalizations,NormalyzerResults-method | Man page |
| performQuantileNormalization | Man page Source code |
| performSMADNormalization | Man page Source code |
| performVSNNormalization | Man page Source code |
| plotBoxPlot | Man page Source code |
| plotCVvsIntensity | Man page Source code |
| plotComparisonVenns | Man page Source code |
| plotContrastPCA | Man page Source code |
| plotContrastPHists | Man page Source code |
| plotCorrelation | Man page Source code |
| plotDendrograms | Man page Source code |
| plotDensity | Man page Source code |
| plotFrontPage | Man page Source code |
| plotMA | Man page Source code |
| plotMDS | Man page Source code |
| plotMeanSD | Man page Source code |
| plotPHist | Man page Source code |
| plotQQ | Man page Source code |
| plotRLE | Man page Source code |
| plotReplicateVarAndStableVariables | Man page Source code |
| plotReplicateVariance | Man page Source code |
| plotSampleOutlierSummary | Man page Source code |
| plotScatter | Man page Source code |
| plotSigScatter | Man page Source code |
| preprocessData | Man page Source code |
| printMeta | Man page Source code |
| printPlots | Man page Source code |
| proteiosToNormalyzer | Source code |
| reduceTechnicalReplicates | Man page Source code |
| setupJobDir | Man page Source code |
| setupModel | Source code |
| setupPlotting | Man page Source code |
| setupRawContrastObject | Man page Source code |
| setupRawDataObject | Man page Source code |
| setupTestData | Man page Source code |
| validateSampleReplication | Man page Source code |
| verifyContrasts | Man page Source code |
| verifyDesignMatrix | Man page Source code |
| verifyMultipleSamplesPresent | Man page Source code |
| verifySummarizedExperiment | Man page Source code |
| verifyValidNumbers | Man page Source code |
| writeNormalizedDatasets | Man page Source code |
