BASiCS (version 1.1.0)

newBASiCS_Chain: Creates a BASiCS_Chain object from pre-computed MCMC chains

Description

BASiCS_Chain creates a '>BASiCS_Chain object from pre-computed MCMC chains.

Usage

newBASiCS_Chain(parameters)

Arguments

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)

Value

An object of class '>BASiCS_Chain.

References

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

See Also

BASiCS_Chain

Examples

# NOT RUN {
Data <- makeExampleBASiCS_Data()
Chain <- BASiCS_MCMC(Data, N = 50, Thin = 5, Burn = 5)

ChainMu <- displayChainBASiCS(Chain, 'mu')
ChainDelta <- displayChainBASiCS(Chain, 'delta')
ChainPhi <- displayChainBASiCS(Chain, 'phi')
ChainS <- displayChainBASiCS(Chain, 's')
ChainNu <- displayChainBASiCS(Chain, 'nu')
ChainTheta <- displayChainBASiCS(Chain, 'theta')

ChainNew <- newBASiCS_Chain(parameters = list(mu = ChainMu, delta = ChainDelta,
                            phi = ChainPhi, s = ChainS, 
                            nu = ChainNu, theta = ChainTheta))

# }