Simulate differential abundance (DA) flow cytometry data

Generates simulated flow cytometry data with differential abundance of a target cell type across treatment groups, batch effects, and multiple abundance settings. Writes per-sample FCS files and returns sample- and cell-level metadata.

Usage

simulate_DA_data(
  groups = c("Baseline", "Depletion"),
  batches = c("Batch1", "Batch2"),
  settings = c(0.005, 0.05, 0.5),
  samples_per_group = 6,
  mean_cells = 50000,
  sd_cells = 500,
  seed = 42,
  output_dir = file.path(tempdir(), "sim_DA_fcs")
)

Arguments

groups

Character vector of treatment group names.

batches

Character vector of batch names.

settings

Numeric vector of proportions for the Baseline group. The non-Baseline group uses half the proportion.

samples_per_group

Integer. Number of samples per group per setting.

mean_cells

Integer. Mean number of cells per sample.

sd_cells

Numeric. Standard deviation of cell count.

seed

Integer. Random seed for reproducibility.

output_dir

Character. Directory path where FCS files are written.

Value

A list with two elements:

sample_meta

A data.frame with one row per sample and columns Sample, Treatment, Batch, Setting, fcs_path.

cell_meta

A data.frame with one row per cell and columns Sample, Treatment, Batch, Setting, CellType.

Examples

if (FALSE) { # \dontrun{
sim <- simulate_DA_data(
  samples_per_group = 2,
  mean_cells = 1000,
  sd_cells = 100,
  output_dir = file.path(tempdir(), "sim_DA_fcs")
)
head(sim$sample_meta)
head(sim$cell_meta)
} # }