doScrubletDetect: doScrubletDetect

In drieslab/Giotto_site_suite: Spatial Single-Cell Transcriptomics Toolbox

doScrubletDetect

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 \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1016/j.cels.2018.11.005")}

drieslab/Giotto_site_suite documentation built on April 26, 2023, 11:51 p.m.