BASiCS (version 0.3.1)

BASiCS_Summary-class: The BASiCS_Summary class

Description

Container of a summary of a BASiCS_Chain-class object. In each slot, first column contains posterior medians, second column contains the lower limits of an high posterior density interval and third column contains the upper limits of high posterior density intervals.

Slots

mu

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

delta

Posterior medians (first column), lower (second column) and upper (third column) limits of gene-specific biological cell-to-cell heterogeneity hyper-parameters \(\delta[i]\), biological genes only

phi

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

s

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

nu

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

theta

Posterior median (first column), lower (second column) and upper (third column) limits of technical variability hyper-parameter \(\theta\) (each row represents one batch)

Examples

# NOT RUN {
# A BASiCS_Summary object created by the Summary method.
Data = makeExampleBASiCS_Data()
MCMC_Output <- BASiCS_MCMC(Data, N = 100, Thin = 2, Burn = 2)
MCMC_Summary <- Summary(MCMC_Output)
# }