Kersplat setup

Setup the parameters required for the Kersplat simulation

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.

Value

A complete KersplatParams object

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.

See also

kersplatGenNetwork, kersplatSelectRegs, kersplatSimGeneMeans, kersplatSimPaths, KersplatParams

Examples

if (requireNamespace("igraph", quietly = TRUE)) {
    params <- kersplatSetup()
}
#> Setting up parameters...
#> Generating gene network...
#> Selecting regulators...
#> Simulating means...
#> Sampling from gamma distribution...
#> Simulating paths...
#> Simulating path 1...