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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.