BASiCS (version 0.7.30)

BASiCS_D_Chain-class: The BASiCS_D_Chain class

Description

Container of an MCMC sample of the BASiCS model parameters when comparing 2 populations of cells. For each population, these are independently generated by the function BASiCS_MCMC and afterwards combined through the function CombineBASiCS_Chain .

Slots

muTest

MCMC chain for gene-specific expression levels \(\mu[i]\) in test group, defined as true input molecules in case of technical genes (matrix with q.bio columns, all elements must be positive numbers)

muRef

MCMC chain for gene-specific expression levels \(\mu[i]\) in reference group, defined as true input molecules in case of technical genes (matrix with q.bio columns, all elements must be positive numbers)

deltaTest

MCMC chain for gene-specific biological cell-to-cell heterogeneity hyper-parameters \(\delta[i]\) in test group, biological genes only (matrix with q columns, all elements must be positive numbers)

deltaRef

MCMC chain for gene-specific biological cell-to-cell heterogeneity hyper-parameters \(\delta[i]\) in reference group, biological genes only (matrix with q columns, all elements must be positive numbers)

phi

MCMC chain for cell-specific mRNA content normalising constants \(\phi[j]\) (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 capture efficiency (or amplification biases if not using UMI based counts) normalising constants \(s[j]\) (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)

thetaTest

MCMC chain for technical variability hyper-parameter \(\theta[test]\) in the test sample (vector, all elements must be positive)

thetaRef

MCMC chain for technical variability hyper-parameter \(\theta[ref]\) in the reference sample (vector, all elements must be positive)

offset

Offset value to capture global changes in mRNA content. Default value = 1 (when no offset correction has been performed)

Examples

# NOT RUN {
# See vignette

# }