| simulate_phenopath {phenopath} | R Documentation |
Simulate synthetic data from the phenopath model, where each gene is sampled from one of four types (see details).
simulate_phenopath(N = 100, G = 40, G_de = NULL, G_pst = NULL, G_pst_beta = NULL, G_de_pst_beta = NULL)
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 |
Will simulate data for a number of genes corresponding to one of four regimes:
de ('differential expression'), where the gene has no association to the latent
trajectory and exhibits differential expression only
pst ('pseudotime'), the gene shows pseudotemporal regulation but no
differential regulation
pst_beta ('pseudotime + beta interactions'), the gene shows pseudotemporal regulation
that is modulated by covariate interactions
de_pst_beta ('differential expression + pseudotime + interactions), all of the above
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.
sim <- simulate_phenopath()