Scrublet Rust interface

Usage

rs_sc_scrublet(
  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().
seed: Integer. Seed for reproducibility purposes.
verbose: Boolean. Controls 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 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 integer vector representing the first parent of the simulated doublets.
pair_2 - Optional integer vector representing the second parent of the simulated doublets.