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GPU: Scrublet doublet detection

rs_sc_scrublet_gpu.Rd

[Experimental] GPU equivalent of bixverse::rs_sc_scrublet. The PCA of the observed cells, the projection of the simulated doublets and the kNN over the combined embedding run on the WGPU backend. HVG selection, doublet simulation, scoring and the Otsu threshold stay on the CPU. Which nearest neighbour index runs is decided by the knn_backend element of scrublet_params.

Usage

rs_sc_scrublet_gpu(
  f_path_gene,
  f_path_cell,
  cells_to_keep,
  scrublet_params,
  seed,
  verbose,
  streaming,
  return_combined_pca,
  return_pairs
)

Arguments

f_path_gene

String. Path to the counts_genes.bin file.

f_path_cell

String. Path to the counts_cells.bin file.

cells_to_keep

Integer vector. The indices (0-indexed!) of the cells to include in this analysis.

scrublet_params

List. Parameter list, see params_scrublet_gpu().

seed

Integer. Seed for reproducibility purposes.

verbose

Integer. 0L - quiet; 1L - normal verbosity; 2L - detailed verbosity.

streaming

Boolean. Shall the data be streamed for the HVG calculations.

return_combined_pca

Boolean. Shall the generated PCA be returned.

return_pairs

Boolean. Shall the parents of the simulated cells be returned.

Value

A list with

  • 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.

References

Wolock, et al., Cell Syst, 2020