BASiCS (version 0.7.30)

BASiCS_D_Summary-class: The BASiCS_D_Summary class contains posterior medians and the limits of the highest posterior density (HPD) interval for all BASiCS model parameters

Description

Container of a summary of a BASiCS_D_Chain-class object.

Slots

muTest

Posterior medians (first column), lower (second column) and upper (third column) limits of HPD interval for gene-specific expression levels \(\mu[i]\) in test group.

muRef

Posterior medians (first column), lower (second column) and upper (third column) limits of HPD interval for gene-specific expression levels \(\mu[i]\) in reference group.

deltaTest

Posterior medians (first column), lower (second column) and upper (third column) limits of HPD interval for gene-specific biological cell-to-cell heterogeneity hyper-parameters \(\delta[i]\) in test group

deltaRef

Posterior medians (first column), lower (second column) and upper (third column) limits of HPD interval for gene-specific biological cell-to-cell heterogeneity hyper-parameters \(\delta[i]\) in reference group

phi

Posterior medians (first column), lower (second column) and upper (third column) limits of HPD interval for cell-specific mRNA content normalising constants \(\phi[j]\)

s

Posterior medians (first column), lower (second column) and upper (third column) limits of HPD interval for cell-specific capture efficiency (or amplification biases if not using UMI based counts) normalising constants \(s[j]\)

of

HPD interval for Posterior medians (first column), lower (second column) and upper (third column) limits of HPD interval for cell-specific random effects \(\nu[j]\)

thetaTest

Posterior median (first column), lower (second column) and upper (third column) limits of HPD interval for technical variability hyper-parameter \(\theta[test]\) for test sample (vector, all elements must be positive)

thetaRef

Posterior median (first column), lower (second column) and upper (third column) limits of HPD interval for technical variability hyper-parameter \(\theta[ref]\) for 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)

probHPD

Posterior probability contained in the HPD interval. Must be a value between 0 and 1.

Examples

# NOT RUN {
# see help(BASiCS_D_MCMC)

# }