Man pages for GabrielHoffman/variancePartition
Quantify and interpret drivers of variation in multilevel gene expression experiments
| applyQualityWeights | Apply pre-specified sample weights |
| as.data.frame.varPartResults | Convert to data.frame |
| as.matrix-varPartResults-method | Convert to matrix |
| augmentPriorCount | Augment observed read counts with prior count |
| BIC.MArrayLM | BIC from model fit |
| BIC.MArrayLM2 | BIC from model fit |
| calcVarPart-method | Compute variance statistics |
| canCorPairs | canCorPairs |
| classifyTestsF | Multiple Testing Genewise Across Contrasts |
| classifyTestsF-MArrayLM2-method | Multiple Testing Genewise Across Contrasts |
| colinearityScore | Collinearity score |
| deviation-method | Deviation from expectation for each observation |
| diffVar-method | Test differential variance |
| 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 |
| dscchisq | Scaled chi-square |
| 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 |
| getContrast-method | Extract contrast matrix for linear mixed model |
| get_prediction-method | Compute predicted value of formula for linear (mixed) model |
| getTreat-method | Test if coefficient is different from a specified value |
| ggColorHue | Default colors for ggplot |
| hatvalues-method | Compute hatvalues |
| isRunableFormula | Test if formula is full rank on this dataset |
| logLik.MArrayLM | Log-likelihood from model fit |
| logLik.MArrayLM2 | Log-likelihood from model fit |
| makeContrastsDream | Construct Matrix of Custom Contrasts |
| MArrayLM2-class | Class MArrayLM2 |
| mvTest_input-class | Class mvTest_input |
| mvTest-method | Multivariate tests on results from 'dream()' |
| plotCompareP-method | Compare p-values from two analyses |
| plotContrasts | Plot representation of contrast matrix |
| plotCorrMatrix | plotCorrMatrix |
| plotCorrStructure | plotCorrStructure |
| plotPercentBars-method | Bar plot of gene fractions |
| plotStratify | plotStratify |
| plotStratifyBy | plotStratifyBy |
| plotVarianceEstimates | Plot Variance Estimates |
| plotVarPart-method | Violin plot of variance fractions |
| rdf | Residual degrees of freedom |
| rdf_from_matrices | Fast approximate residual degrees of freedom |
| rdf.merMod | Approximate residual degrees of freedom |
| reOnly | Adapted from lme4:::reOnly |
| residuals.MArrayLM2 | Residuals for result of dream |
| residuals-MArrayLM2-method | residuals for MArrayLM2 |
| residuals-MArrayLM-method | residuals for MArrayLM |
| residuals-VarParFitList-method | Residuals from model fit |
| shrinkageMetric | Shrinkage metric for eBayes |
| sortCols-method | Sort variance partition statistics |
| subset.MArrayLM2-method | Subseting for MArrayLM2 |
| toptable-method | Table of Top Genes from Linear Model Fit |
| VarParCIList-class | Class VarParCIList |
| VarParFitList-class | Class VarParFitList |
| varParFrac-class | Class varParFrac |
| varPartConfInf | Linear mixed model confidence intervals |
| varPartData | Simulation dataset for examples |
| varPartDEdata | A simulated dataset of gene counts |
| varPartResults-class | Class varPartResults |
| vcov-MArrayLM2-method | Co-variance matrix for 'dream()' fit |
| vcov-MArrayLM-method | Co-variance matrix for 'dream()' fit |
| vcovSqrt-method | Sqrt of co-variance matrix for 'dream()' fit |
| voomWithDreamWeights | Transform RNA-Seq Data Ready for Linear Mixed Modelling with... |
