BASiCS_Chain {BASiCS} | R Documentation |
Container of an MCMC sample of the BASiCS' model parameters
(see Vallejos et al, 2015) as generated by the
function BASiCS_MCMC
.
parameters
List of matrices containing MCMC chains for each model parameter.
MCMC chain for gene-specific mean expression parameters
μ_i, biological genes only
(matrix with q.bio
columns, all elements must be positive numbers)
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)
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
)
MCMC chain for cell-specific technical normalisation parameters
s_j (matrix with n
columns,
all elements must be positive numbers)
MCMC chain for cell-specific random effects ν_j
(matrix with n
columns, all elements must be positive numbers)
MCMC chain for technical over-dispersion parameter(s) θ (matrix, all elements must be positive, each colum represents 1 batch)
Catalina A. Vallejos cnvallej@uc.cl
Vallejos, Marioni and Richardson (2015). PLoS Computational Biology.
# A BASiCS_Chain object created by the BASiCS_MCMC function. Data <- makeExampleBASiCS_Data() Chain <- BASiCS_MCMC(Data, N = 100, Thin = 2, Burn = 2)