scrublet_R: Scrublet

In scfurl/m3addon: This package adds to the popular "monocle3"

Description

See preprint: Scrublet: computational identification of cell doublets in single-cell transcriptomic data Samuel L Wolock, Romain Lopez, Allon M Klein. bioRxiv 357368; doi: https://doi.org/10.1101/357368

Usage

scrublet_R(
  cds,
  python_home = system("which python", intern = TRUE),
  return_results_only = FALSE,
  min_counts = 2,
  min_cells = 3,
  expected_doublet_rate = 0.06,
  min_gene_variability_pctl = 85,
  n_prin_comps = 50,
  sim_doublet_ratio = 2,
  n_neighbors = NULL
)

Arguments

cds	the CellDataSet upon which to perform Scrublet
python_home	The python home directory where Scrublet is installed
return_results_only	bool (optional, default False)
min_counts,	int (optional, default=2), See scrublet reference
min_cells,	int (optional, default=3), See scrublet reference
expected_doublet_rate,	float (optional, default=0.06), See scrublet reference - expected_doublet_rate: the fraction of transcriptomes that are doublets, typically 0.05-0.1. Results are not particularly sensitive to this parameter. For this example, the expected doublet rate comes from the Chromium User Guide: https://support.10xgenomics.com/permalink/3vzDu3zQjY0o2AqkkkI4CC
min_gene_variability_pctl,	int (optional, default=85), See scrublet reference
n_prin_comps,	int (optional, default=50), See scrublet reference (Number of principal components to use)
sim_doublet_ratio,	int (optional, default=2), the number of doublets to simulate, relative to the number of observed transcriptomes. This should be high enough that all doublet states are well-represented by simulated doublets. Setting it too high is computationally expensive. The default value is 2, though values as low as 0.5 give very similar results for the datasets that have been tested.
n_neighbors,	int (optional) n_neighbors: Number of neighbors used to construct the KNN classifier of observed transcriptomes and simulated doublets. The default value of round(0.5*sqrt(n_cells)) generally works well. Return only a list containing scrublet output

Value

The input CellDataSet with an additional column added to pData with both the doublet_score output from scrublet, and

scfurl/m3addon documentation built on Aug. 9, 2021, 5:30 p.m.