BASiCS (version 1.1.0)

BASiCS_Chain: The BASiCS_Chain class

Description

Container of an MCMC sample of the BASiCS' model parameters (see Vallejos et al, 2015) as generated by the function BASiCS_MCMC.

Slots

parameters

List of matrices containing MCMC chains for each model parameter.

mu

MCMC chain for gene-specific mean expression parameters \(\mu_i\), biological genes only (matrix with q.bio columns, all elements must be positive numbers)

delta

MCMC chain for gene-specific biological over-dispersion parameters \(\delta_i\), biological genes only (matrix with q.bio columns, all elements must be positive numbers)

phi

MCMC chain for cell-specific mRNA content normalisation parameters \(\phi_j\) (matrix with n columns, all elements must be positive numbers and the sum of its elements must be equal to n)

s

MCMC chain for cell-specific technical normalisation parameters \(s_j\) (matrix with n columns, all elements must be positive numbers)

nu

MCMC chain for cell-specific random effects \(\nu_j\) (matrix with n columns, all elements must be positive numbers)

theta

MCMC chain for technical over-dispersion parameter(s) \(\theta\) (matrix, all elements must be positive, each colum represents 1 batch)

References

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

Examples

# NOT RUN {
# A BASiCS_Chain object created by the BASiCS_MCMC function.
Data <- makeExampleBASiCS_Data()
Chain <- BASiCS_MCMC(Data, N = 100, Thin = 2, Burn = 2)

# }