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

### References

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

### See Also

`BASiCS_Chain`

### Examples

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

    DR <- BASiCS_DenoisedRates(Data, Chain)

[Package BASiCS version 1.0.1 Index]