BASiCS (version 1.1.0)

BASiCS_DenoisedCounts: Calculates denoised expression expression counts

Description

Calculates denoised expression counts by removing cell-specific technical variation.

Usage

BASiCS_DenoisedCounts(Data, Chain)

Arguments

Data

an object of class '>SingleCellExperiment

Chain

an object of class '>BASiCS_Chain

Value

A matrix of denoised expression counts. In line with global scaling normalisation strategies, these are defined as \(X_{ij}/(\phi_j \nu_j)\) for biological genes and \(X_{ij}/(\nu_j)\) for spike-in genes. For this calculation \(\phi_j\) \(\nu_j\) are estimated by their corresponding posterior medians.

Details

See vignette

References

Vallejos, Marioni and Richardson (2015). PLoS Computational Biology.

See Also

'>BASiCS_Chain

Examples

# NOT RUN {
Data <- makeExampleBASiCS_Data(WithSpikes = TRUE)
Chain <- BASiCS_MCMC(Data, N = 10000, Thin = 10, Burn = 5000, 
                     PrintProgress = FALSE)

DC <- BASiCS_DenoisedCounts(Data, Chain)

# }