simulate_initialData: Simulate Initial Data

In MethEvolSIM: Simulate DNA Methylation Dynamics on Different Genomic Structures along Genealogies

Simulate Initial Data

Description

This function simulates initial data based on the provided information and parameters.

Usage

simulate_initialData(
  infoStr,
  params = NULL,
  CFTP = FALSE,
  CFTP_step_limit = 327680000
)

Arguments

infoStr	A data frame containing columns 'n' for the number of sites, and 'globalState' for the favoured global methylation state. If customized equilibrium frequencies are given, it also contains columns 'u_eqFreq', 'p_eqFreq' and 'm_eqFreq' with the equilibrium frequency values for unmethylated, partially methylated and methylated.
params	Optional data frame with specific parameter values.
CFTP	Default FALSE. TRUE for calling cftp algorithm to set root state according to model equilibrium (Note that current implementation neglects IWE process). Structure as in get_parameterValues() output. If not provided, default values will be used.
CFTP_step_limit	when CFTP = TRUE, maximum number of steps before applying an approximation method (default 327680000 corresponding to size of CFTP info of approx 6.1 GB).

Details

The function performs several checks on the input data and parameters to ensure they meet the required criteria and simulates DNA methylation data.

Value

A list containing the simulated data ($data) and parameters ($params).

Examples

# Example data
infoStr <- data.frame(n = c(10, 100, 10), globalState = c("M", "U", "M"))

# Simulate initial data  with default parameters
simulate_initialData(infoStr = infoStr)

# Simulate data evolution along a tree with custom parameters
custom_params <- get_parameterValues()
custom_params$iota <- 0.5
simulate_initialData(infoStr = infoStr, params = custom_params)

MethEvolSIM documentation built on April 12, 2025, 1:30 a.m.