Quantify and interpret drivers of variation in multilevel gene expression experiments

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Documentation for package ‘variancePartition’ version 1.35.4

• 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()'