doScrubletDetect#

Date

2022-10-06

https://github.com/drieslab/Giotto/tree/suite/R/python_scrublet.R#L18

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#

Argument

Description

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

Seealso#

This function wraps the python package scrublet c(“\Sexpr[results=rd]{tools:::Rd_expr_doi(“#1”)}?, “10.1016/j.cels.2018.11.005?) list(“tools:::Rd_expr_doi(“10.1016/j.cels.2018.11.005”)?)