simulate_phenopath {phenopath} | R Documentation

## Simulate from phenopath model

### Description

Simulate synthetic data from the phenopath model, where each gene is sampled from one of four types (see details).

### Usage

    simulate_phenopath(N = 100, G = 40, G_de = NULL, G_pst = NULL,
      G_pst_beta = NULL, G_de_pst_beta = NULL)

### Arguments

`N` | Number of samples to simulate
`G` | Number of genes to simulate. Should be divisible by 4
`G_de` | Number of genes to simulate from the differential expression regime
`G_pst` | Number of genes to simulate from the pseudotime regime
`G_pst_beta` | Number of genes to simulate from the pseudotime + beta interactions regime
`G_de_pst_beta` | Number of genes to simulate from the differential expression + pseudotime + interactions regime

### Details

Will simulate data for a number of genes corresponding to one of four regimes:

1. `de` ('differential expression'), where the gene has no association to the latent trajectory and exhibits differential expression only

2. `pst` ('pseudotime'), the gene shows pseudotemporal regulation but no differential regulation

3. `pst_beta` ('pseudotime + beta interactions'), the gene shows pseudotemporal regulation that is modulated by covariate interactions

4. `de_pst_beta` ('differential expression + pseudotime + interactions), all of the above

### Value

A list with four entries:

- `parameters` A `tibble` with an entry for each gene and a column for each parameter value and simulation regime (see details).

- `y` The N-by-G simulated gene expression matrix.

- `x` The N-length vector of covariates.

- `z` The N-length vector of pseudotimes.

### Examples

    sim <- simulate_phenopath()

[Package phenopath version 1.6.7 Index]