Skip to contents

Single cell test data

generate_single_cell_test_data.Rd

This function generates synthetic data for single cell test purposes. These data can be used for testing functionality of various single cell functions.

Usage

generate_single_cell_test_data(
  syn_data_params = params_sc_synthetic_data(),
  seed = 42L
)

Arguments

syn_data_params

List. Contains the parameters for the generation of synthetic data, see: params_sc_synthetic_data(). Has the following elements:

  • n_cells - Integer. Number of cells.

  • n_genes - Integer. Number of genes.

  • marker_genes - List. A nested list that indicates which gene indices are markers for which cell.

  • n_batches - Integer. Number of batches.

  • batch_effect_strength - String. Indicates the strength of the batch effect to add.

seed

Integer. The seed for the generation of the seed data.

Value

List with the following items

  • counts - dgRMatrix with cells x genes.

  • obs - data.table that contains the cell information.

  • var - data.table that contains the var information.

Examples

# a small synthetic experiment with three planted cell types
data <- generate_single_cell_test_data(
  syn_data_params = params_sc_synthetic_data(n_cells = 200L, n_genes = 40L)
)
dim(data$counts)
#> [1] 200  40
head(data$obs, 3)
#>     cell_id    cell_grp batch_index
#>      <char>      <char>       <num>
#> 1: cell_001 cell_type_1           1
#> 2: cell_002 cell_type_2           1
#> 3: cell_003 cell_type_3           1