Run doublet-calling with scds

Usage

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

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".
data_type: Optional precomputed result from CheckDataType for the input assay. Primarily used internally to avoid repeated scans of the same count matrix across nested QC calls.
...: Additional arguments to be passed to scds::cxds_bcds_hybrid().
verbose: Whether to print the message. Default is TRUE.

Examples

data(pancreas_sub)
pancreas_sub <- standard_scop(pancreas_sub)
pancreas_sub <- db_scds(pancreas_sub, method = "hybrid")
CellDimPlot(
  pancreas_sub,
  reduction = "umap",
  group.by = "db.scds_hybrid_class"
)

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