Man pages for variancePartition
Quantify and interpret divers of variation in multilevel gene expression experiments
| as.data.frame-varPartResults-method | Convert to data.frame |
| as.matrix-varPartResults-method | Convert to matrix |
| calcVarPart-method | Compute variance statistics |
| canCorPairs | canCorPairs |
| classifyTestsF | Multiple Testing Genewise Across Contrasts |
| classifyTestsF-MArrayLM2-method | Multiple Testing Genewise Across Contrasts |
| colinearityScore | Collinearity score |
| dot-getAllUniContrasts | Get all univariate contrasts |
| dot-isMixedModelFormula | Check if model contains a random effect |
| dot-standard_transform | Compute standard post-processing values |
| dream-method | Differential expression with linear mixed model |
| eBayesFMT | Empirical Bayes Fully Moderated t-statistics |
| eBayes-method | eBayes for MArrayLM2 |
| ESS-method | Effective sample size |
| extractVarPart | Extract variance statistics |
| fitExtractVarPartModel-method | Fit linear (mixed) model, report variance fractions |
| fitVarPartModel-method | Fit linear (mixed) model |
| FMT | Fully moderated t-test |
| FMT-class | Class FMT |
| FMT.ZI | Fully moderated t-test for zero-inflated variances |
| getContrast-method | Extract contrast matrix for linear mixed model |
| get_prediction-method | Compute predicted value of formula for linear (mixed) model |
| ggColorHue | Default colors for ggplot |
| MArrayLM2-class | Class MArrayLM2 |
| plotCompareP-method | Compare p-values from two analyses |
| plotContrasts | Plot representation of contrast matrix |
| plotCorrMatrix | plotCorrMatrix |
| plotCorrStructure | plotCorrStructure |
| plotPercentBars | Bar plot of variance fractions |
| plotStratify | plotStratify |
| plotStratifyBy | plotStratifyBy |
| plotVarPart-method | Violin plot of variance fractions |
| residuals-MArrayLM2-method | residuals for MArrayLM2 |
| residuals-MArrayLM-method | residuals for MArrayLM |
| residuals-VarParFitList-method | Residuals from model fit |
| sortCols-method | Sort variance partition statistics |
| subset.MArrayLM2-method | Subseting for MArrayLM2 |
| toptable-method | toptable for definition |
| VarParCIList-class | Class VarParCIList |
| VarParFitList-class | Class VarParFitList |
| varParFrac-class | Class varParFrac |
| varPartConfInf | Linear mixed model confidence intervals |
| varPartData | Simulation dataset for examples |
| varPartDEdata | Simulation dataset for dream example |
| varPartResults-class | Class varPartResults |
| voomWithDreamWeights | Transform RNA-Seq Data Ready for Linear Mixed Modelling with... |
