BASiCS_DenoisedCounts {BASiCS} | R Documentation

## 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`

### 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.

### 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)

    DC <- BASiCS_DenoisedCounts(Data, Chain)

[Package BASiCS version 1.0.1 Index]