BASiCS (version 1.1.0)

BASiCS_DenoisedRates: Calculates denoised expression rates

Description

Calculates normalised and denoised expression rates, by removing the effect of technical variation.

Usage

BASiCS_DenoisedRates(Data, Chain, Propensities = FALSE)

Arguments

Data

an object of class '>SingleCellExperiment

Chain

an object of class '>BASiCS_Chain

Propensities

If TRUE, returns underlying expression propensitites \(\rho_{ij}\). Otherwise, denoised rates \(\mu_i \rho_{ij}\) are returned. Default: Propensities = FALSE.

Value

A matrix of denoised expression rates (biological genes only)

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)

DR <- BASiCS_DenoisedRates(Data, Chain)

# }