BASiCS_DenoisedRates {BASiCS} | R Documentation

## 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 ρ_{ij}. Otherwise, denoised rates μ_i ρ_{ij} are returned. Default: `Propensities = FALSE`.

### Details

See vignette

### Value

A matrix of denoised expression rates (biological genes only)

### Author(s)

Catalina A. Vallejos cnvallej@uc.cl

Nils Eling eling@ebi.ac.uk

### See Also

`BASiCS_Chain`

### Examples

    Data <- makeExampleBASiCS_Data(WithSpikes = TRUE)
    ## The N and Burn parameters used here are optimised for speed
    ## and should not be used in regular use.
    ## For more useful parameters,
    ## see the vignette (\code{browseVignettes("BASiCS")})
    Chain <- BASiCS_MCMC(Data, N = 1000, Thin = 10, Burn = 500,
                         Regression = FALSE, PrintProgress = FALSE)

    DR <- BASiCS_DenoisedRates(Data, Chain)

[Package BASiCS version 1.99.1 Index]