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:

Examples

sim <- simulate_phenopath()

[Package phenopath version 1.18.0 Index]