BASiCS_DenoisedCounts {BASiCS} | R Documentation |
Calculates denoised expression counts by removing cell-specific technical variation. The latter includes global-scaling normalisation and therefore no further normalisation is required.
BASiCS_DenoisedCounts(Data, Chain, WithSpikes = TRUE)
Data |
An object of class |
Chain |
An object of class |
WithSpikes |
A logical scalar specifying whether denoised spike-in
genes should be generated as part of the output value. This only applies
when the |
See vignette browseVignettes("BASiCS")
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.
Catalina A. Vallejos cnvallej@uc.cl
Nils Eling eling@ebi.ac.uk
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) DC <- BASiCS_DenoisedCounts(Data, Chain)