create_synthetic {mfa} | R Documentation

## Create synthetic data

### Description

Create synthetic bifurcating data for two branches. Optionally incorporate zero inflation and transient gene expression.

### Usage

    create_synthetic(C = 100, G = 40, p_transient = 0, zero_negative = TRUE,
      model_dropout = FALSE, lambda = 1)

### Arguments

`C` | Number of cells to simulate
`G` | Number of genes to simulate
`p_transient` | Propotion of genes that exhibit transient expression
`zero_negative` | Logical: should expression generated less than zero be set to zero? This will zero-inflate the data
`model_dropout` | Logical: if true, expression will be set to zero with the exponential dropout formula dependent on the latent expression using dropout parameter `lambda`
`lambda` | The dropout parameter

### Value

A list with the following entries:

- `X` A cell-by-feature expression matrix

- `branch` A vector of length `C` assigning cells to branches

- `pst` A vector of pseudotimes for each cell

- `k` The k parameters

- `phi` The φ parameters

- `delta` The δ parameters

- `p_transient` The proportion of genes simulated as transient according to the original function call

### Examples

    synth <- create_synthetic()

[Package mfa version 1.16.3 Index]