Default parameters for generation of synthetic CellSweep data

Shapes the fixture with a planted ambient profile that generate_cellsweep_test_data() builds. The defaults give 600 real barcodes over 3 cell types plus 2000 empty droplets, on 200 genes.

Usage

params_sc_synthetic_cellsweep(
  n_real = 600L,
  n_empty = 2000L,
  n_genes = 200L,
  n_celltypes = 3L,
  n_markers = 20L,
  marker_weight = 25,
  ambient_dominance = 0.6,
  alpha_mean = 0.3,
  alpha_sd = 0.12,
  real_lib_size = 3000L,
  empty_lib_size = 120L
)

Arguments

n_real

Integer. Number of real barcodes. Cell types are assigned round-robin over them. Defaults to 600L.

n_empty

Integer. Number of empty droplets. The ambient profile is estimated off these, so at least 30 and preferably a lot more. Defaults to 2000L.

n_genes

Integer. Number of genes. Defaults to 200L.

n_celltypes

Integer. Number of cell types. Defaults to 3L.

n_markers

Integer. Width of each cell type's marker block. The blocks are contiguous and disjoint, so n_markers * n_celltypes has to fit into n_genes. Defaults to 20L.

marker_weight

Numeric. Enrichment of a marker gene over background in its own cell type's profile. Must exceed 1. Defaults to 25.0.

ambient_dominance

Numeric. Fraction of the soup coming from the first cell type. The remainder is flat background. Defaults to 0.6.

alpha_mean

Numeric. Mean planted ambient fraction across real barcodes. Defaults to 0.3.

alpha_sd

Numeric. Spread of the planted ambient fraction. Defaults to 0.12.

real_lib_size

Integer. Expected library size of a real barcode. Defaults to 3000L.

empty_lib_size

Integer. Expected library size of an empty droplet. Defaults to 120L.

Value

A named list with the following elements:

• n_real - Integer. Number of real barcodes. Cell types are assigned round-robin over them. Defaults to 600L.

• n_empty - Integer. Number of empty droplets. The ambient profile is estimated off these, so at least 30 and preferably a lot more. Defaults to 2000L.

• n_genes - Integer. Number of genes. Defaults to 200L.

• n_celltypes - Integer. Number of cell types. Defaults to 3L.

• n_markers - Integer. Width of each cell type's marker block. The blocks are contiguous and disjoint, so n_markers * n_celltypes has to fit into n_genes. Defaults to 20L.

• marker_weight - Numeric. Enrichment of a marker gene over background in its own cell type's profile. Must exceed 1. Defaults to 25.0.

• ambient_dominance - Numeric. Fraction of the soup coming from the first cell type. The remainder is flat background. Defaults to 0.6.

• alpha_mean - Numeric. Mean planted ambient fraction across real barcodes. Defaults to 0.3.

• alpha_sd - Numeric. Spread of the planted ambient fraction. Defaults to 0.12.

• real_lib_size - Integer. Expected library size of a real barcode. Defaults to 3000L.

• empty_lib_size - Integer. Expected library size of an empty droplet. Defaults to 120L.

Details

The soup is the first cell type plus flat background rather than a mixture of every cell type profile. A soup sitting in the span of the cell type profiles makes the contamination fraction unidentifiable, and the fixture would then be testing the repulsion term rather than the model.