newBASiCS_Chain {BASiCS} | R Documentation |
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
μ_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 δ_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
φ_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 ν_j
(matrix with n columns, all elements must be positive numbers)
- theta
MCMC chain for technical over-dispersion parameter(s)
θ (matrix, all elements must be positive,
each colum represents 1 batch)
|
Value
An object of class BASiCS_Chain
.
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()
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))
[Package
BASiCS version 1.0.1
Index]