Variance-Aware Evaluation of Batch Correction

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Documentation for package ‘BatchVaria’ version 0.99.2

• DESCRIPTION file
• User guides, package vignettes and other documentation
• Package NEWS
• Package README

Help Pages

assayVariance	Total variance of each assay
availableCorrectionMethods	Available correction methods
availableVarianceMethods	Available variance profiling methods
basisProjection	Sample coordinates on a reference assay's principal axes
basisRetention	Variance retained on a reference assay's principal axes
BatchVaria-requirements	Requirements BatchVaria places on a SummarizedExperiment
compareCorrelations	Compare sample correlation structure across assays
comparePCA	Compare PCA variance structure across assays
evaluateCorrections	Evaluate batch correction performance across assays
exampleBatchVaria	Example BatchVaria dataset with batch and biological effects
newVarianceSummary	Build a conforming variance summary
plotBasisProjection	Plot samples projected onto a reference assay's basis
plotBatchEntropy	Plot batch mixing entropy
plotCorrelationChange	Plot correlation preservation after correction
plotPCATrajectory	Plot PCA correction trajectories
plotSampleDistance	Plot sample distance heatmap
plotVarianceComposition	Plot variance composition across model terms
plotVarianceDelta	Plot variance change relative to baseline
plotVarianceRadar	Radar plot of variance redistribution
profileVariance	Profile sources of variance in expression data
provenance	Report the analysis history recorded on an object
recordVariance	Record variance decomposition results
registerCorrectionMethod	Register a batch correction method
registerVarianceEngine	Register a variance profiling engine
runCorrection	Apply batch correction to expression data
unregisterCorrectionMethod	Remove a registered batch correction method
unregisterVarianceEngine	Remove a registered variance profiling engine
varianceChange	Summarise variance change vs raw for a model term
varianceDelta	Compute variance redistribution relative to baseline
varianceHistory	Access variance profiling history
varianceResults	Retrieve variance decomposition results
varianceTable	Create variance summary tables