doScrubletDetect#

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Last Updated: Mar 11, 2023

Description#

run scrublet doublet detection for raw expression.

Usage#

doScrubletDetect(
  gobject,
  feat_type = NULL,
  spat_unit = "cell",
  expression_values = "raw",
  expected_doublet_rate = 0.06,
  min_counts = 1,
  min_cells = 1,
  min_gene_variability_pctl = 85,
  n_prin_comps = 30,
  return_gobject = TRUE
)

Arguments#

`gobject`	giotto object containing expression data
`feat_type`	feature type
`spat_unit`	spatial unit
`expression_values`	expression values to use
`expected_doublet_rate`	expected transcriptomes that are doublets. 0.06 is from 10x Chromium guide.
`min_counts`	scrublet internal data filtering, min counts found to be considered a cell
`min_cells`	scrublet internal data filtering. min cells expressed to be considered a feat
`min_gene_variability_pctl`	scrublet internal PCA generation. highly variable gene percentile cutoff
`n_prin_comps`	number of PCs to use in PCA for detection
`return_gobject`	return as gobject if TRUE, data.frame with cell_ID if FALSE

Value#

list including doublet scores and classifications

See Also#

This function wraps the python package scrublet doi:10.1016/j.cels.2018.11.005