kersplatSetup {splatter} | R Documentation

## Kersplat setup

### Description

Setup the parameters required for the Kersplat simulation

### Usage

    kersplatSetup(params = newKersplatParams(), verbose = TRUE, ...)

### Arguments

`params` | KersplatParams object containing simulation parameters.
`verbose` | logical. Whether to print progress messages
`...` | any additional parameter settings to override what is provided in `params`.

### Details

The first stage is a two-step Kersplat simulation is to generate some of the intermediate parameters. The resulting parameters allow multiple simulated datasets to be generated from the same biological structure (using `kersplatSample`). As with all the other parameters these values can be manually overwritten if desired.

The setup involves the following steps:

1. Generate a gene network (if not already present)

2. Select regulator genes (if not already present)

3. Simulate gene means (if not already present)

4. Simulate cell paths

The resulting `KersplatParams` object will have the following parameters set (if they weren't already).

- `mean.values`

- `network.graph`

- `network.regsSet`

- `paths.means`

See `KersplatParams` for more details about these parameters and the functions for the individual steps for more details about the process.

### Value

A complete KersplatParams object

### See Also

`kersplatGenNetwork`, `kersplatSelectRegs`, `kersplatSimGeneMeans`, `kersplatSimPaths`, `KersplatParams`

### Examples

    if (requireNamespace("igraph", quietly = TRUE)) {
        params <- kersplatSetup()
    }

[Package splatter version 1.12.0 Index]