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Simulate Count Data for Microbiome Studies

Source: R/simulate.R
countdata_sim_fun.Rd

This function simulates count data for microbiome studies based on log mean, log fold change, and dispersion parameters. It supports generating data for multiple simulations and allows flexibility in specifying the number of control and treatment samples or samples per group.

Usage

countdata_sim_fun(
  logmean_param,
  logfoldchange_param,
  dispersion_param,
  nsamp_per_group = NULL,
  ncont = NULL,
  ntreat = NULL,
  notu,
  nsim = 1,
  disp_scale = 0.3,
  max_lfc = 15,
  maxlfc_iter = 1000,
  seed = NULL
)

Arguments

logmean_param

A list of parameters for simulating the log mean abundance.

logfoldchange_param

A list of parameters for simulating log fold change, containing:

  • par: Optimal parameters for log fold change fitting.

  • np: Number of components for the log fold change model.

  • sd_ord: Order of the polynomial for the standard deviation parameter.

dispersion_param

A list of dispersion parameters containing:

  • asymptDisp: Asymptotic dispersion parameter.

  • extraPois: Additional Poisson variation parameter.

nsamp_per_group

Number of samples per group (control and treatment). If provided, ncont and ntreat must not be specified.

ncont

Number of control samples. Specify along with ntreat when nsamp_per_group is not provided.

ntreat

Number of treatment samples. Specify along with ncont when nsamp_per_group is not provided.

notu

Number of operational taxonomic units (OTUs) to simulate.

nsim

Number of simulations to run. Default is 1.

disp_scale

Scale parameter for the dispersion. Default is 0.3.

max_lfc

Maximum allowable log fold change. Default is 15.

maxlfc_iter

Maximum number of iterations for ensuring log fold change is within max_lfc. Default is 1,000.

seed

Seed value for reproducibility. Default is NULL.

Value

A list containing:

  • countdata_list: A list of count data matrices for each simulation.

  • metadata_list: A list of metadata data frames for each simulation.

  • logmean_list: A list of log mean vectors for each simulation.

  • logfoldchange_list: A list of log fold change vectors for each simulation.

  • treat_countdata_list: A list of treatment count data matrices for each simulation.

  • control_countdata_list: A list of control count data matrices for each simulation.

Examples

# Load required packages
library(foreach)
library(doParallel)
#> Loading required package: iterators
#> Loading required package: parallel
# Define parameters
logmean_param <- list(mu = 0, sigma = 1)
logfoldchange_param <- list(par = rnorm(11), np = 2, sd_ord = 2)
dispersion_param <- list(asymptDisp = 0.1, extraPois = 0.05)

# Simulate count data
result <- countdata_sim_fun(
  logmean_param = logmean_param,
  logfoldchange_param = logfoldchange_param,
  dispersion_param = dispersion_param,
  nsamp_per_group = 10,
  notu = 50,
  nsim = 2,
  seed = 123
)
#> 
#> Attaching package: ‘purrr’
#> The following objects are masked from ‘package:foreach’:
#> 
#>     accumulate, when
#> mixtools package, version 2.0.0.1, Released 2022-12-04
#> This package is based upon work supported by the National Science Foundation under Grant No. SES-0518772 and the Chan Zuckerberg Initiative: Essential Open Source Software for Science (Grant No. 2020-255193).

# Access simulation results
countdata <- result$countdata_list[[1]]
metadata <- result$metadata_list[[1]]