BASiCS_Chain {BASiCS} | R Documentation

## The BASiCS_Chain class

### Description

Container of an MCMC sample of the BASiCS' model parameters (see Vallejos et al, 2015) as generated by the function `BASiCS_MCMC`.

### Slots

`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)

### Author(s)

Catalina A. Vallejos cnvallej@uc.cl

### References

Vallejos, Marioni and Richardson (2015). PLoS Computational Biology.

### Examples

    # A BASiCS_Chain object created by the BASiCS_MCMC function.
    Data <- makeExampleBASiCS_Data()
    Chain <- BASiCS_MCMC(Data, N = 100, Thin = 2, Burn = 2)

[Package BASiCS version 1.0.1 Index]