Quantify and interpret drivers of variation in multilevel gene
expression experiments
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Documentation for package ‘variancePartition’ version 1.32.5
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 |
| 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 |
| 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()' |