BASiCS_DenoisedCounts {BASiCS}R Documentation

Calculates denoised expression expression counts

Description

Calculates denoised expression counts by removing cell-specific technical variation. The latter includes global-scaling normalisation and therefore no further normalisation is required.

Usage

BASiCS_DenoisedCounts(Data, Chain)

Arguments

Data

an object of class SingleCellExperiment

Chain

an object of class BASiCS_Chain

Details

See vignette

Value

A matrix of denoised expression counts. In line with global scaling normalisation strategies, these are defined as X_{ij}/(φ_j ν_j) for biological genes and X_{ij}/(ν_j) for spike-in genes. For this calculation φ_j ν_j are estimated by their corresponding posterior medians. If spike-ins are not used, φ_j is set equal to 1.

Author(s)

Catalina A. Vallejos cnvallej@uc.cl

Nils Eling eling@ebi.ac.uk

See Also

BASiCS_Chain

Examples


Data <- makeExampleBASiCS_Data(WithSpikes = TRUE)
Chain <- BASiCS_MCMC(Data, N = 10000, Thin = 10, Burn = 5000, 
                     Regression = FALSE, PrintProgress = FALSE)

DC <- BASiCS_DenoisedCounts(Data, Chain)


[Package BASiCS version 1.2.1 Index]