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Doublet detection with Scrublet

scrublet_sc.Rd

This function implements the doublet detection from Scrublet, see Wolock, et al. Briefly, arteficial doublets are being generated from the data via random combination of initial cells. Highly variable genes (HVG) are being identified and the observed cells are being projected on a PCA space. Subsequently, the simulated doublets are being projected on the same PCA space given the same HVGs; kNN graphs are being generated and a kNN classifier is used to assign a probability that a given cell in the original data is a doublet. For more details, please check the publication.

Usage

scrublet_sc(
  object,
  scrublet_params = params_scrublet(),
  seed = 42L,
  streaming = FALSE,
  return_combined_pca = FALSE,
  return_pairs = FALSE,
  .verbose = TRUE
)

Arguments

object

SingleCells class.

scrublet_params

A list with the final scrublet parameters, see params_scrublet() for full details.

seed

Integer. Random seed.

streaming

Boolean. Shall streaming be used during the HVG calculations. Slower, but less memory usage.

return_combined_pca

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

return_pairs

Boolean. Shall the pairs be returned.

.verbose

Boolean. Controls verbosity of the function.

Value

A scrublet_res class that has with the following items:

  • predicted_doublets - Boolean vector indicating which observed cells 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. Should roughly match the expected 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

Wollock, et al., Cell Syst, 2020