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Doublet detection with Scrublet on the GPU

scrublet_gpu_sc.Rd

GPU counterpart of bixverse::scrublet_sc(). Three stages run on the WGPU backend: the randomised sparse SVD of the observed cells, the projection of the simulated doublets into that PC space, and the kNN over the combined embedding. HVG selection, doublet simulation, the kNN classifier and the Otsu threshold stay on the CPU, so the speedup tracks how much of the run the SVD and the kNN own. That share grows with cell count: the combined embedding is (1 + sim_doublet_ratio) * n_cells rows tall and an exhaustive kNN over it is quadratic.

Usage

scrublet_gpu_sc(
  object,
  scrublet_params = params_scrublet_gpu(),
  seed = 42L,
  streaming = NULL,
  cells_to_use = NULL,
  group_by = NULL,
  return_combined_pca = FALSE,
  return_pairs = FALSE,
  .verbose = TRUE
)

Arguments

object

SingleCells class from bixverse.

scrublet_params

List. Output of params_scrublet_gpu().

seed

Integer. Random seed.

streaming

Optional boolean. Shall the counts be streamed during HVG selection. If NULL, resolved from the cell count.

cells_to_use

Optional character vector. Names of the cells to run on. The returned object covers exactly these cells.

group_by

Optional string. Column in the obs table to run the method per level of, typically a sample identifier.

return_combined_pca

Boolean. Shall the combined PCA of observed cells and simulated doublets be returned.

return_pairs

Boolean. Shall the parent indices of the simulated doublets be returned.

.verbose

Boolean or integer. Controls verbosity and returns run times. FALSE -> quiet, TRUE or 1L -> normal verbosity, 2L -> detailed verbosity.

Value

A ScrubletRes S3 object, identical in shape to the CPU one, with the following items:

  • predicted_doublets - Boolean vector indicating which observed cells were predicted as doublets (TRUE = doublet, FALSE = singlet).

  • doublet_scores_obs - Numerical vector with the likelihood of being a doublet for the observed cells.

  • doublet_scores_sim - Numerical vector with the likelihood of being a doublet for the simulated cells.

  • doublet_errors_obs - Numerical vector with the standard errors of the scores for the observed cells.

  • z_scores - Z-scores for the observed cells. Represents: score - threshold / error.

  • threshold - Used threshold.

  • detected_doublet_rate - Fraction of cells that are called as doublet.

  • detectable_doublet_fraction - Fraction of simulated doublets with scores above the threshold.

  • overall_doublet_rate - Estimated overall doublet rate.

  • pca - Optional PCA embeddings across the original cells and simulated doublets.

  • pair_1 - Optional index of the parent cell 1 of the simulated doublets.

  • pair_2 - Optional index of the parent cell 2 of the simulated doublets.

The 0-indexed cell indices are attached as the cell_indices attribute. Grouped runs additionally carry grouped and group_by_col attributes and a cell_groups element.

Details

Scores do not match the CPU bit for bit. The SVD is randomised on both sides but draws a different sketch, and the GPU indices break neighbour ties differently. Expect a correlation around 0.99 rather than equality, and a handful of borderline calls to flip because Otsu's threshold is a step function of the histogram bins.

References

Wolock, et al., Cell Syst, 2020