Simulate Log Fold Change Values — logfoldchange_sim

This function generates simulated log fold change (LFC) values based on the provided log mean abundance and LFC parameters. The simulation ensures that the generated LFC values remain within a specified maximum range by iterating until convergence or until a maximum iteration limit is reached.

Usage

logfoldchange_sim_fun(
  logmean_sim,
  logfoldchange_param,
  max_lfc = 15,
  max_iter = 10000,
  seed = 121
)

Arguments

logmean_sim

A numeric vector of simulated log mean abundances.

logfoldchange_param

A list containing parameters for the log fold change simulation:

par: Optimal parameters for the log fold change fit.
np: Optimal number of components for the log fold change model.
sd_ord: Order of the polynomial used for the standard deviation parameter of the log fold change.

max_lfc

A numeric value specifying the maximum allowable absolute log fold change value. Default is 15.

max_iter

An integer specifying the maximum number of iterations allowed to ensure all simulated LFC values are within the max_lfc range. Default is 10,000.

seed

random-number seed

Value

A numeric vector of simulated log fold change values (lfc).

Examples

set.seed(101)
# Define simulated log mean abundance
logmean_sim <- rnorm(100, mean = 0, sd = 1)

# Define parameters for log fold change simulation
logfoldchange_param <- list(
  par = rnorm(11),       # Example parameters
  np = 2,                # Number of components
  sd_ord = 2             # Order of polynomial for SD
)

# Simulate log fold change values
logfoldchange_sim_fun(
  logmean_sim = logmean_sim,
  logfoldchange_param = logfoldchange_param,
  max_lfc = 10,
  max_iter = 5000
)
#>   [1]  0.77536534 -0.75927908  0.57559853  0.24988592  1.29554742  3.20377118
#>   [7]  0.47951965 -0.39424034  3.08421259  3.45909061  0.07150158  1.74829991
#>  [13] -1.14778645  1.44999231  2.08759275  2.67255845  1.42411340 -0.94717905
#>  [19]  4.33031343  0.70459024  0.45920383  3.14750041  2.02422422  1.23460892
#>  [25]  2.43004015  1.54934384  2.46467222  1.99330437 -0.45609681  3.11060255
#>  [31]  0.16023216  2.57254352  3.25793035  0.60396932  1.10901345  1.37469207
#>  [37]  2.92895477  0.20506906  4.04637355  2.02622178 -0.43806886  2.50240781
#>  [43]  0.29248446  0.64951982  0.78484957  1.50003440 -0.01191195 -5.98171420
#>  [49] -2.94150866  2.62317835  1.30759331  0.71860840  0.68786991  0.61950167
#>  [55]  2.03931987  1.75635258  2.97146597  3.13447579  2.77627194  2.49630360
#>  [61]  0.09310071  1.06172800  1.06209385 -0.17932371  2.48775509  2.70721117
#>  [67]  3.06653638  0.52568456  2.00110377 -2.77202494  2.35125799  3.37302253
#>  [73]  0.28443019  1.71850784  1.06309408  1.29522830  2.30808053  0.35606973
#>  [79] -0.19398176 -0.96092257  3.57141184  0.67600711  2.93379296  2.35866360
#>  [85]  0.04805865  2.67475960  2.91065453  0.88217677  2.54776601  3.02793378
#>  [91]  3.51039604  1.25352899 -5.75334804 -1.21701458 -1.37136417  1.56562167
#>  [97] -0.64715531  0.95082237 -0.18732567  1.68143967