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Parameters for identifying empty droplets

params_sc_empty_droplets.Rd

CellSweep trains its ambient profile on the empty droplets, so it needs them called before it runs. Four ways to do that, in descending order of how much you should trust them. "supplied" takes an existing logical column from the obs table. This is the common case: if you have CellRanger's filtered barcode list you already know which barcodes are empty, and nothing here will beat that. "umi_cutoff" calls everything below an absolute library size empty. "expected_cells" turns a cell count into that cutoff via the sorted library sizes. "knee" finds the cutoff from the curvature of the rank / log-count curve; it is experimental in the reference too, and smoothing puts the curvature minimum a few ranks ahead of the actual cliff, so it sweeps up the real barcodes nearest the transition.

Usage

params_sc_empty_droplets(
  method = c("supplied", "umi_cutoff", "expected_cells", "knee"),
  is_empty_column = NULL,
  umi_cutoff = NULL,
  expected_cells = NULL
)

Arguments

method

String. How the empty droplets are called, see the description. One of c("supplied", "umi_cutoff", "expected_cells", "knee"). Defaults to "supplied".

is_empty_column

String or NULL. Name of the logical obs column holding the mask. Required for method = "supplied", ignored otherwise. Defaults to NULL.

umi_cutoff

Integer or NULL. Barcodes with a library size strictly below this are empty. Required for method = "umi_cutoff", ignored otherwise. Defaults to NULL.

expected_cells

Integer or NULL. Number of real cells expected in the run. Required for method = "expected_cells", ignored otherwise. Defaults to NULL.

Value

A named list with the following elements:

  • method - String. How the empty droplets are called, see the description. One of c("supplied", "umi_cutoff", "expected_cells", "knee"). Defaults to "supplied".

  • is_empty_column - String or NULL. Name of the logical obs column holding the mask. Required for method = "supplied", ignored otherwise. Defaults to NULL.

  • umi_cutoff - Integer or NULL. Barcodes with a library size strictly below this are empty. Required for method = "umi_cutoff", ignored otherwise. Defaults to NULL.

  • expected_cells - Integer or NULL. Number of real cells expected in the run. Required for method = "expected_cells", ignored otherwise. Defaults to NULL.