Package: variancePartition 1.35.4

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:Gabriel Hoffman [aut, cre]

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variancePartition.pdf |variancePartition.html✨
variancePartition/json (API)
NEWS

# 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

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-1.35.1(bioc 3.20)variancePartition-1.34.0(bioc 3.19)

bioconductor-package

43 exports 2.86 score 97 dependencies 3 dependents 25 mentions

Last updated 27 days agofrom:4540193c4e

Exports:[.MArrayLM2 applyQualityWeights as.matrix augmentPriorCount calcVarPart canCorPairs colinearityScore deviation diffVar dream eBayes ESS extractVarPart fitExtractVarPartModel fitVarPartModel get_prediction getContrast getTreat ggColorHue hatvalues isRunableFormula makeContrastsDream mvTest plotCompareP plotContrasts plotCorrMatrix plotCorrStructure plotPercentBars plotStratify plotStratifyBy plotVarianceEstimates plotVarPart rdf rdf.merMod residuals residuals.MArrayLM2 shrinkageMetric sortCols topTable varPartConfInf vcov vcovSqrt voomWithDreamWeights

Dependencies:aod backports BH Biobase BiocGenerics BiocParallel bitops boot brio broom callr caTools cli codetools colorspace corpcor cpp11 crayon desc diffobj digest dplyr EnvStats evaluate fANCOVA fansi farver formatR fs futile.logger futile.options generics ggplot2 glue gplots gtable gtools isoband iterators jsonlite KernSmooth labeling lambda.r lattice lifecycle limma lme4 lmerTest magrittr MASS Matrix matrixStats mgcv minqa munsell mvtnorm nlme nloptr nortest numDeriv pbkrtest pillar pkgbuild pkgconfig pkgload plyr praise processx ps purrr R6 rbibutils RColorBrewer Rcpp RcppArmadillo RcppEigen Rdpack remaCor rematch2 reshape2 RhpcBLASctl rlang rprojroot scales snow statmod stringi stringr testthat tibble tidyr tidyselect utf8 vctrs viridisLite waldo withr

Variance partitioning analysis

Developed by Gabriel Hoffman

Rendered fromvariancePartition.Rmdusingknitr::rmarkdownon Jun 14 2024.

Last update: 2023-08-18
Started: 2023-08-18

Additional visualizations of variance structure

Developed by Gabriel Hoffman

Rendered fromadditional_visualization.Rmdusingknitr::rmarkdownon Jun 14 2024.

Last update: 2023-08-18
Started: 2019-07-08

Theory and practice of random effects

Developed by Gabriel Hoffman

Rendered fromrnd_effects.Rmdusingknitr::rmarkdownon Jun 14 2024.

Last update: 2023-08-18
Started: 2023-06-21

dream analysis

Developed by Gabriel Hoffman

Rendered fromdream.Rmdusingknitr::rmarkdownon Jun 14 2024.

Last update: 2024-05-31
Started: 2018-06-11

Error handling

Developed by Gabriel Hoffman

Rendered fromerrors.Rmdusingknitr::rmarkdownon Jun 14 2024.

Last update: 2023-09-05
Started: 2023-08-18

Frequently asked questions

Developed by Gabriel Hoffman

Rendered fromFAQ.Rmdusingknitr::rmarkdownon Jun 14 2024.

Last update: 2023-09-05
Started: 2020-06-13

Multivariate tests

Developed by Gabriel Hoffman

Rendered frommvtests.Rmdusingknitr::rmarkdownon Jun 14 2024.

Last update: 2023-09-05
Started: 2023-06-21

Citation

Development and contributors

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 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

Package: variancePartition 1.35.4

variancePartition: Quantify and interpret drivers of variation in multilevel gene expression experiments

Variance partitioning analysis

Additional visualizations of variance structure

Theory and practice of random effects

dream analysis

Error handling

Frequently asked questions

Multivariate tests

Citation

Development and contributors

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)