Default parameters for generation of synthetic single cell data (ADT)

For the generation of synthetic single cell data mostly for testing or showcasing purposes. In this case, ADT counts to test multi-modal integration. The default configurations generates 1000 cells x 15 proteins with probes 1:3 being cell markers for cell type 1, genes 4:6 for cell type 2 and genes 7:9 for cell type. Columns 13:15 represents isotype controls.

Usage

params_sc_synthetic_data_adt(
  n_cells = 1000L,
  n_proteins = 15L,
  n_batches = 1L,
  marker_genes = list(cell_type_1 = list(marker_genes = 0:2), cell_type_2 =
    list(marker_genes = 3:5), cell_type_3 = list(marker_genes = 6:8)),
  isotype_controls = 12:14,
  batch_effect_strength = c("strong", "medium", "weak")
)

Arguments

n_cells

Integer. Number of cells. Defaults to 1000L.

n_proteins

Integer. Number of proteins Defaults to 15L.

n_batches

Integer. Number of batches. Defaults to 1L.

marker_genes

Any. A nested list that indicates which gene indices are markers for which cell. Defaults to list(cell_type_1 = list(marker_genes = 0:2), cell_type_2 = list(marker_genes = 3:5), cell_type_3 = list(marker_genes = 6:8)).

isotype_controls

Integer vector. The columns that defines the isotype controls. (0-indexed!) Defaults to 12:14.

batch_effect_strength

String. The strength of the batch effect to add. One of c("strong", "medium", "weak"). Defaults to "strong".

Value

A named list with the following elements:

• n_cells - Integer. Number of cells. Defaults to 1000L.

• n_proteins - Integer. Number of proteins Defaults to 15L.

• marker_genes - Any. A nested list that indicates which gene indices are markers for which cell. Defaults to list(cell_type_1 = list(marker_genes = 0:2), cell_type_2 = list(marker_genes = 3:5), cell_type_3 = list(marker_genes = 6:8)).

• n_batches - Integer. Number of batches. Defaults to 1L.

• isotype_controls - Integer vector. The columns that defines the isotype controls. (0-indexed!) Defaults to 12:14.

• batch_effect_strength - String. The strength of the batch effect to add. One of c("strong", "medium", "weak"). Defaults to "strong".