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Single cell test data (ADT)

generate_single_cell_test_data_adt.Rd

This function generates synthetic ADT counts for single cell test purposes. These data can be used for testing multi-modal functionality of various single cell functions. Pairs cell-for-cell with generate_single_cell_test_data() when generated with matching n_cells, number of cell types and n_batches.

Usage

generate_single_cell_test_data_adt(
  syn_data_params = params_sc_synthetic_data_adt(),
  seed = 42L
)

Arguments

syn_data_params

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

  • n_cells - Integer. Number of cells.

  • n_proteins - Integer. Number of proteins.

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

  • n_batches - Integer. Number of batches.

  • isotype_controls - Integer vector. Column indices (0-based) of the isotype controls.

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

seed

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

Value

List with the following items

  • counts - Numeric matrix with cells x proteins.

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

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

Examples

# synthetic ADT counts, cell-for-cell with the RNA generator
adt <- generate_single_cell_test_data_adt()
dim(adt$counts)
#> [1] 1000   15
head(adt$var, 3)
#>    protein_id is_isotype
#>        <char>     <lgcl>
#> 1: protein_01      FALSE
#> 2: protein_02      FALSE
#> 3: protein_03      FALSE