doScrubletDetect#
Last Updated: Oct 02, 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#
|
giotto object containing expression data |
|
feature type |
|
spatial unit |
|
expression values to use |
|
expected transcriptomes that are doublets. 0.06 is from 10x Chromium guide. |
|
scrublet internal data filtering, min counts found to be considered a cell |
|
scrublet internal data filtering. min cells expressed to be considered a feat |
|
scrublet internal PCA generation. highly variable gene percentile cutoff |
|
number of PCs to use in PCA for detection |
|
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