Introduction | Input data | Running an analysis | Standard application | Saving plot to file | Plot expression stratified by other variables | Intuition about the backend | Interpretation | Should a variable be modeled as fixed or random effect? | Which variables should be included? | Assess correlation between all pairs of variables | Advanced analysis | Extracting additional information from model fits | Removing batch effects before fitting model | Variation within multiple subsets of the data | Detecting problems caused by collinearity of variables | Including weights computed separately | Including interaction terms | Application to expression data | Gene-level counts | limma::voom() | DESeq2 | Isoform quantification | tximport | Compare with other methods | Tissue is major source of variation | Individual is major source of variation | Statistical details | Implementation in R | Interpretation of percent variance explained | Variation with multiple subsets of the data | Variance partitioning and differential expression | Modelling error in gene expression measurements | Session Info | References
Package: variancePartition 1.43.1
Gabriel E. Hoffman
variancePartition: Quantify and interpret drivers of variation in multilevel gene expression experiments
Quantify and interpret multiple sources of biological and technical variation in gene expression experiments. Uses a linear mixed model to quantify variation in gene expression attributable to individual, tissue, time point, or technical variables. Includes dream differential expression analysis for repeated measures.
Authors:
variancePartition_1.43.1.tar.gz
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variancePartition_1.43.1.tgz(r-4.6-any)variancePartition_1.43.1.tgz(r-4.5-any)
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variancePartition_1.43.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
variancePartition/json (API)
| # Install 'variancePartition' in R: |
| install.packages('variancePartition', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/diseaseneurogenomics/variancepartition/issues
Pkgdown/docs site:https://diseaseneurogenomics.github.io
Datasets:
- countMatrix - A simulated dataset of gene counts
- geneCounts - Simulation dataset for examples
- geneExpr - Simulation dataset for examples
- info - Simulation dataset for examples
- metadata - A simulated dataset of gene counts
On BioConductor:variancePartition-1.43.1(bioc 3.24)variancePartition-1.42.0(bioc 3.23)
rnaseqgeneexpressiongenesetenrichmentdifferentialexpressionbatcheffectqualitycontrolregressionepigeneticsfunctionalgenomicstranscriptomicsnormalizationpreprocessingmicroarrayimmunooncologysoftware
Last updated from:97c8bfeab0. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 271 | ||
| linux-devel-x86_64 | NOTE | 670 | ||
| source / vignettes | OK | 746 | ||
| linux-release-x86_64 | NOTE | 606 | ||
| macos-release-arm64 | NOTE | 473 | ||
| macos-oldrel-arm64 | NOTE | 382 | ||
| windows-devel | NOTE | 509 | ||
| windows-release | NOTE | 532 | ||
| windows-oldrel | NOTE | 540 | ||
| wasm-release | OK | 222 |
Exports:[.MArrayLM2applyQualityWeightsas.matrixaugmentPriorCountcalcVarPartcanCorPairscolinearityScoredeviationdiffVardreameBayesESSextractVarPartfitExtractVarPartModelfitVarPartModelget_predictiongetContrastgetTreatggColorHuehatvaluesisRunableFormulamakeContrastsDreammvTestplotComparePplotContrastsplotCorrMatrixplotCorrStructureplotPercentBarsplotStratifyplotStratifyByplotVarianceEstimatesplotVarPartrdfrdf.merModresidualsresiduals.MArrayLM2shrinkageMetricsortColstopTablevarPartConfInfvcovvcovSqrtvoomWithDreamWeights
Dependencies:aodbackportsBHBiobaseBiocGenericsBiocParallelbitopsbootbroomcaToolsclicodetoolscolorspacecorpcorcowplotcpp11DerivdoBydplyrEnvStatsfANCOVAfarverforecastformatRfracdifffutile.loggerfutile.optionsgenericsggplot2gluegplotsgtablegtoolsisobanditeratorsKernSmoothlabelinglambda.rlatticelifecyclelimmalme4lmerTestlmtestmagrittrMASSMatrixmatrixStatsmicrobenchmarkminqamodelrmvtnormnlmenloptrnnetnortestnumDerivpbkrtestpillarpkgconfigplyrpurrrR6rbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRdpackreformulasremaCorreshape2RhpcBLASctlrlangS7scalessnowstatmodstringistringrtibbletidyrtidyselecttimeDateurcautf8vctrsviridisLitewithrzoo
Variance partitioning analysis
Last update: 2026-05-11
Started: 2023-08-18
dream analysis
Standard RNA-seq processing | Limma Analysis | Dream Analysis | Advanced hypothesis testing | Using contrasts to compare coefficients | Comparing multiple coefficients | Joint hypothesis test of multiple coefficients | Small-sample method | variancePartition plot | Comparing p-values | Parallel processing | Session info | References
Last update: 2024-05-31
Started: 2018-06-11
Error handling
Errors in dream() | Gene-level errors | Shared by multiple functions | Warnings | Errors | Errors: Problems removing samples with NA/NaN/Inf values | Errors with BiocParallel multithreading backend | globally specify that all multithreading using bpiterate from BiocParallel | should use 8 cores | Session Info
Last update: 2023-09-05
Started: 2023-08-18
Frequently asked questions
Interperting the residual variance | Current GitHub issues | Session Info
Last update: 2023-09-05
Started: 2020-06-13
Multivariate tests
Import transcript-level counts | Standard dream analysis | Multivariate analysis | Gene set analysis | Session info | References
Last update: 2023-09-05
Started: 2023-06-21
Additional visualizations of variance structure
Plot variance structure | By Individual | Reorder samples | Original order of samples | By Tissue | By Individual and Tissue | Session Info
Last update: 2023-08-18
Started: 2019-07-08
Theory and practice of random effects
variancePartition | Estimating contributions to expression variation | dream | Hypothesis testing | Session Info
Last update: 2023-08-18
Started: 2023-06-21
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Apply pre-specified sample weights | applyQualityWeights |
| Convert to data.frame | as.data.frame.varPartResults |
| Convert to matrix | as.matrix as.matrix,varPartResults-method |
| Augment observed read counts with prior count | augmentPriorCount |
| BIC from model fit | BIC.MArrayLM |
| BIC from model fit | BIC.MArrayLM2 |
| Compute variance statistics | calcVarPart calcVarPart,glm-method calcVarPart,glmer-method calcVarPart,glmerMod-method calcVarPart,lm-method calcVarPart,lmerMod-method calcVarPart,negbin-method |
| canCorPairs | canCorPairs |
| Multiple Testing Genewise Across Contrasts | classifyTestsF |
| Multiple Testing Genewise Across Contrasts | classifyTestsF,MArrayLM2-method |
| Collinearity score | colinearityScore |
| Deviation from expectation for each observation | deviation deviation,MArrayLM-method |
| Test differential variance | diffVar diffVar,MArrayLM-method |
| Differential expression with linear mixed model | dream |
| Scaled chi-square | dscchisq |
| eBayes generic for for MArrayLM and MArrayLM2 | eBayes |
| eBayes for MArrayLM | eBayes,MArrayLM-method |
| eBayes for MArrayLM2 | eBayes,MArrayLM2-method |
| Effective sample size | ESS ESS,lmerMod-method |
| Extract variance statistics | extractVarPart |
| Fit linear (mixed) model, report variance fractions | fitExtractVarPartModel fitExtractVarPartModel,data.frame-method fitExtractVarPartModel,EList-method fitExtractVarPartModel,ExpressionSet-method fitExtractVarPartModel,matrix-method fitExtractVarPartModel,sparseMatrix-method |
| Fit linear (mixed) model | fitVarPartModel fitVarPartModel,data.frame-method fitVarPartModel,EList-method fitVarPartModel,ExpressionSet-method fitVarPartModel,matrix-method fitVarPartModel,sparseMatrix-method |
| Compute predicted value of formula for linear (mixed) model | get_prediction get_prediction,lm-method get_prediction,lmerMod-method |
| Extract contrast matrix for linear mixed model | getContrast |
| Test if coefficient is different from a specified value | getTreat getTreat,MArrayLM-method getTreat,MArrayLM2-method |
| Default colors for ggplot | ggColorHue |
| Compute hatvalues | hatvalues,MArrayLM-method hatvalues,MArrayLM2-method |
| Test if formula is full rank on this dataset | isRunableFormula |
| Log-likelihood from model fit | logLik.MArrayLM |
| Log-likelihood from model fit | logLik.MArrayLM2 |
| Construct Matrix of Custom Contrasts | makeContrastsDream |
| Class MArrayLM2 | MArrayLM2-class |
| Multivariate tests on results from 'dream()' | mvTest mvTest,MArrayLM,EList,integer-method mvTest,MArrayLM,EList,list-method mvTest,MArrayLM,EList,missing-method mvTest,MArrayLM,EList,vector-method mvTest,MArrayLM,matrix,ANY-method mvTest,MArrayLM,matrix-method mvTest,mvTest_input,ANY,ANY-method mvTest,mvTest_input,method |
| Class mvTest_input | mvTest_input-class |
| Compare p-values from two analyses | plotCompareP |
| Plot representation of contrast matrix | plotContrasts |
| plotCorrMatrix | plotCorrMatrix |
| plotCorrStructure | plotCorrStructure |
| Bar plot of gene fractions | plotPercentBars plotPercentBars,data.frame-method plotPercentBars,matrix-method plotPercentBars,varPartResults-method |
| plotStratify | plotStratify |
| plotStratifyBy | plotStratifyBy |
| Plot Variance Estimates | plotVarianceEstimates |
| Violin plot of variance fractions | plotVarPart plotVarPart,data.frame-method plotVarPart,matrix-method plotVarPart,varPartResults-method |
| Residual degrees of freedom | rdf |
| Fast approximate residual degrees of freedom | rdf_from_matrices |
| Approximate residual degrees of freedom | rdf.merMod |
| Adapted from lme4:::reOnly | reOnly |
| residuals for MArrayLM | residuals,MArrayLM-method |
| residuals for MArrayLM2 | residuals,MArrayLM2-method |
| Residuals from model fit | residuals,VarParFitList-method |
| Residuals for result of dream | residuals.MArrayLM2 |
| Shrinkage metric for eBayes | shrinkageMetric |
| Sort variance partition statistics | sortCols sortCols,data.frame-method sortCols,matrix-method sortCols,varPartResults-method |
| Table of Top Genes from Linear Model Fit | topTable topTable,MArrayLM-method toptable,MArrayLM-method topTable,MArrayLM2-method toptable,MArrayLM2-method |
| Class VarParCIList | VarParCIList-class |
| Class VarParFitList | VarParFitList-class |
| Class varParFrac | varParFrac-class |
| Linear mixed model confidence intervals | varPartConfInf |
| Simulation dataset for examples | geneCounts geneExpr info varPartData |
| A simulated dataset of gene counts | countMatrix metadata varPartDEdata |
| Class varPartResults | varPartResults-class |
| Co-variance matrix for 'dream()' fit | vcov,MArrayLM-method |
| Co-variance matrix for 'dream()' fit | vcov,MArrayLM2-method |
| Sqrt of co-variance matrix for 'dream()' fit | mvTest,MArrayLM-method mvTest,MArrayLM2-method vcovSqrt vcovSqrt,MArrayLM-method vcovSqrt,MArrayLM2-method |
| Transform RNA-Seq Data Ready for Linear Mixed Modelling with 'dream()' | voomWithDreamWeights |
