KersplatParams {splatter} | R Documentation

## The KersplatParams class

### Description

S4 class that holds parameters for the Kersplat simulation.

### Parameters

The Kersplat simulation uses the following parameters:

`nGenes`

  The number of genes to simulate.

`nCells`

  The number of cells to simulate.

`[seed]`

  Seed to use for generating random numbers.

Mean parameters
  `mean.shape`

    Shape parameter for the mean gamma distribution.

  `mean.rate`

    Rate parameter for the mean gamma distribution.

  `mean.outProb`

    Probability that a gene is an expression outlier.

  `mean.outFacLoc`

    Location (meanlog) parameter for the expression outlier factor log-normal distribution.

  `mean.outFacScale`

    Scale (sdlog) parameter for the expression outlier factor log-normal distribution.

  `mean.dens`

    `density` object describing the log gene mean density.

  `[mean.method]`

    Method to use for simulating gene means. Either "fit" to sample from a gamma distribution (with expression outliers) or "density" to sample from the provided density object.

  `[mean.values]`

    Vector of means for each gene.

Biological Coefficient of Variation parameters
  `bcv.common`

    Underlying common dispersion across all genes.

  `[bcv.df]`

    Degrees of Freedom for the BCV inverse chi-squared distribution.

Network parameters
  `[network.graph]`

    Graph containing the gene network.

  `[network.nRegs]`

    Number of regulators in the network.

Paths parameters
  `[paths.programs]`

    Number of expression programs.

  `[paths.design]`

    data.frame describing path structure. See `kersplatSimPaths` for details.

Library size parameters
  `lib.loc`

    Location (meanlog) parameter for the library size log-normal distribution, or mean parameter if a normal distribution is used.

  `lib.scale`

    Scale (sdlog) parameter for the library size log-normal distribution, or sd parameter if a normal distribution is used.

  `lib.dens`

    `density` object describing the library size density.

  `[lib.method]`

    Method to use for simulating library sizes. Either "fit" to sample from a log-normal distribution or "density" to sample from the provided density object.

Design parameters
  `[cells.design]`

    data.frame describing cell structure. See `kersplatSimCellMeans` for details.

Doublet parameters
  `[doublet.prop]`

    Proportion of cells that are doublets.

Ambient parameters
  `[ambient.scale]`

    Scaling factor for the library size log-normal distribution when generating ambient library sizes.

  `[ambient.nEmpty]`

    Number of empty cells to simulate.

The parameters not shown in brackets can be estimated from real data using `kersplatEstimate`. For details of the Kersplat simulation see `kersplatSimulate`.

[Package splatter version 1.12.0 Index]