# Quantify and interpret divers of variation in multilevel gene expression experiments

## Documentation for package ‘variancePartition’ version 1.17.10

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

.getAllUniContrasts | Get all univariate contrasts
.isMixedModelFormula | Check if model contains a random effect
.standard_transform | Compute standard post-processing values
as.data.frame | Convert to data.frame
as.data.frame-method | Convert to data.frame
as.matrix | Convert to matrix
as.matrix-method | Convert to matrix
calcVarPart | Compute variance statistics
calcVarPart-method | Compute variance statistics
canCorPairs | canCorPairs
classifyTestsF | Multiple Testing Genewise Across Contrasts
classifyTestsF-method | Multiple Testing Genewise Across Contrasts
colinearityScore | Collinearity score
countMatrix | Simulation dataset for dream example
dream | Differential expression with linear mixed model
eBayes-method | eBayes for MArrayLM2
ESS | Effective sample size
ESS-method | Effective sample size
extractVarPart | Extract variance statistics
fitExtractVarPartModel | Fit linear (mixed) model, report variance fractions
fitExtractVarPartModel-method | Fit linear (mixed) model, report variance fractions
fitVarPartModel | Fit linear (mixed) model
fitVarPartModel-method | Fit linear (mixed) model
geneCounts | Simulation dataset for examples
geneExpr | Simulation dataset for examples
getContrast | Extract contrast matrix for linear mixed model
getVarianceComponents | Extract variance terms
ggColorHue | Default colors for ggplot
info | Simulation dataset for examples
MArrayLM2-class | Class MArrayLM2
metadata | Simulation dataset for dream example
plotCompareP | 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 | Violin plot of variance fractions
plotVarPart-method | Violin plot of variance fractions
residuals | Residuals from model fit
residuals-method | Residuals from model fit
residuals-method | residuals for MArrayLM2
sortCols | Sort variance partition statistics
sortCols-method | Sort variance partition statistics
subset.MArrayLM2-method | Subseting for MArrayLM2
topTable-method | toptable for MArrayLMM_lmer
toptable-method | toptable for MArrayLMM_lmer
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 dream()
[.MArrayLM2 | Subseting for MArrayLM2