simulate_phenopath: Simulate from phenopath model

In phenopath: Genomic trajectories with heterogeneous genetic and environmental backgrounds

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()

Example output

Warning messages:
1: `as_data_frame()` is deprecated as of tibble 2.0.0.
Please use `as_tibble()` instead.
The signature and semantics have changed, see `?as_tibble`.
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated. 
2: The `x` argument of `as_tibble.matrix()` must have unique column names if `.name_repair` is omitted as of tibble 2.0.0.
Using compatibility `.name_repair`.
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated. 

phenopath documentation built on Nov. 8, 2020, 6:53 p.m.