BASiCS_DenoisedRates: Calculates denoised expression rates
In catavallejos/BASiCS: Bayesian Analysis of Single-Cell Sequencing data

BASiCS_DenoisedRates

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 `\rho_{ij}`. Otherwise, denoised rates `\mu_i \rho_{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

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)

catavallejos/BASiCS documentation built on March 27, 2024, 12:49 a.m.