Run doublet-calling with scds — db_scds • scop

This function performs doublet-calling using the scds package on a Seurat object.

Usage

db_scds(
  srt,
  assay = "RNA",
  db_rate = ncol(srt)/1000 * 0.01,
  method = c("hybrid", "cxds", "bcds"),
  ...
)

Arguments

srt: A Seurat object.
assay: The name of the assay to be used for doublet-calling. Default is "RNA".
db_rate: The expected doublet rate. Default is calculated as ncol(srt) / 1000 * 0.01.
method: The method to be used for doublet-calling. Options are "hybrid", "cxds", or "bcds".
...: Additional arguments to be passed to scds::cxds_bcds_hybrid function.

Examples

data("pancreas_sub")
pancreas_sub <- db_scds(pancreas_sub, method = "hybrid")
CellDimPlot(
  srt = pancreas_sub,
  reduction = "umap",
  group.by = "db.scds_hybrid_class"
)
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's fill values.

FeatureDimPlot(
  srt = pancreas_sub,
  reduction = "umap", features = "db.scds_hybrid_score"
)