BIC.MArrayLM            BIC from model fit
BIC.MArrayLM2           BIC from model fit
ESS                     Effective sample size
MArrayLM2-class         Class MArrayLM2
VarParCIList-class      Class VarParCIList
VarParFitList-class     Class VarParFitList
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
calcVarPart             Compute variance statistics
canCorPairs             canCorPairs
classifyTestsF          Multiple Testing Genewise Across Contrasts
classifyTestsF,MArrayLM2-method
                        Multiple Testing Genewise Across Contrasts
colinearityScore        Collinearity score
deviation               Deviation from expectation for each observation
diffVar                 Test differential variance
dream                   Differential expression with linear mixed model
dscchisq                Scaled chi-square
eBayes,MArrayLM2-method
                        eBayes for MArrayLM2
extractVarPart          Extract variance statistics
fitExtractVarPartModel
                        Fit linear (mixed) model, report variance
                        fractions
fitVarPartModel         Fit linear (mixed) model
getContrast             Extract contrast matrix for linear mixed model
getTreat                Test if coefficient is different from a
                        specified value
get_prediction          Compute predicted value of formula for linear
                        (mixed) model
ggColorHue              Default colors for ggplot
hatvalues,MArrayLM-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
mvTest                  Multivariate tests on results from 'dream()'
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
plotStratify            plotStratify
plotStratifyBy          plotStratifyBy
plotVarPart             Violin plot of variance fractions
plotVarianceEstimates   Plot Variance Estimates
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,MArrayLM-method
                        residuals for MArrayLM
residuals,MArrayLM2-method
                        residuals for MArrayLM2
residuals,VarParFitList-method
                        Residuals from model fit
residuals.MArrayLM2     Residuals for result of dream
shrinkageMetric         Shrinkage metric for eBayes
sortCols                Sort variance partition statistics
topTable                Table of Top Genes from Linear Model Fit
varParFrac-class        Class varParFrac
varPartConfInf          Linear mixed model confidence intervals
varPartDEdata           A simulated dataset of gene counts
varPartData             Simulation dataset for examples
varPartResults-class    Class varPartResults
vcov,MArrayLM-method    Co-variance matrix for 'dream()' fit
vcov,MArrayLM2-method   Co-variance matrix for 'dream()' fit
vcovSqrt                Sqrt of co-variance matrix for 'dream()' fit
voomWithDreamWeights    Transform RNA-Seq Data Ready for Linear Mixed
                        Modelling with 'dream()'
