Function to model simulation with wisp

This function fits a wisp model to an attractor-based simulation dataset and extracts the estimated functional spatial effects, replicate random effects, and p-values for functional spatial effects. It then compiles these results along with the ground-truth values from the simulation for comparison.

Usage

model_attractor_simulation_wisp(
  sim,
  sim_num,
  LRO_cost = "none",
  bs_num = 1000,
  max_fork = 1
)

Arguments

sim

A list object returned by the attractor_simulation function, containing the simulation data and parameters.

sim_num

An integer specifying the simulation number for setting the random seed and labeling results.

LRO_cost

Passed to the wisp function. Character string giving cost function to use when evaluating likelihood-ratio outlier (LRO) parameters for testing for expression-rate transition points in the data ("AIC", "BIC", "NLL"; anything else defaults to the hand-specified LROcutoff and LROwindow_factor).

bs_num

An integer specifying the number of bootstrap resamples to run.

max_fork

An integer specifying the number of forks to run when computing bootstraps in parallel. For Windows, must be 1.

Value

A data frame containing the estimated values (est), ground-truth values (true), parameter types (param), parameter-associated gene or replicate (id), modeling method used (method), and simulation number (sim).