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

## Documentation for package ‘variancePartition’ version 1.39.0

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

## Help Pages

applyQualityWeights | Apply pre-specified sample weights
as.data.frame.varPartResults | Convert to data.frame
as.matrix | Convert to matrix
as.matrix-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 | 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 | A simulated dataset of gene counts
deviation | Deviation from expectation for each observation
deviation-method | Deviation from expectation for each observation
diffVar | Test differential variance
diffVar-method | Test differential variance
dream | Differential expression with linear mixed model
dscchisq | Scaled chi-square
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
getTreat | Test if coefficient is different from a specified value
getTreat-method | Test if coefficient is different from a specified value
get_prediction | Compute predicted value of formula for linear (mixed) model
get_prediction-method | Compute predicted value of formula for linear (mixed) model
ggColorHue | Default colors for ggplot
hatvalues-method | Compute hatvalues
info | Simulation dataset for examples
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
metadata | A simulated dataset of gene counts
mvTest | Multivariate tests on results from 'dream()'
mvTest,mvTest_input,method | Multivariate tests on results from 'dream()'
mvTest-method | Multivariate tests on results from 'dream()'
mvTest-method | Sqrt of co-variance matrix for 'dream()' fit
mvTest_input-class | Class mvTest_input
plotCompareP | Compare p-values from two analyses
plotContrasts | Plot representation of contrast matrix
plotCorrMatrix | plotCorrMatrix
plotCorrStructure | plotCorrStructure
plotPercentBars | Bar plot of gene fractions
plotPercentBars-method | Bar plot of gene fractions
plotStratify | plotStratify
plotStratifyBy | plotStratifyBy
plotVarianceEstimates | Plot Variance Estimates
plotVarPart | Violin plot of variance fractions
plotVarPart-method | Violin plot of variance fractions
rdf | Residual degrees of freedom
rdf.merMod | Approximate residual degrees of freedom
rdf_from_matrices | Fast approximate residual degrees of freedom
reOnly | Adapted from lme4:::reOnly
residuals-method | residuals for MArrayLM
residuals-method | residuals for MArrayLM2
residuals-method | Residuals from model fit
residuals.MArrayLM2 | Residuals for result of dream
shrinkageMetric | Shrinkage metric for eBayes
sortCols | Sort variance partition statistics
sortCols-method | Sort variance partition statistics
topTable | Table of Top Genes from Linear Model Fit
topTable-method | Table of Top Genes from Linear Model Fit
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-method | Co-variance matrix for 'dream()' fit
vcov-method | Co-variance matrix for 'dream()' fit
vcovSqrt | Sqrt of 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 'dream()'