Run doublet-calling with scds — db

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")
#> Warning: The following arguments are not used: drop
#> Warning: The following arguments are not used: drop
#> Error in as.vector(data): no method for coercing this S4 class to a vector
CellDimPlot(pancreas_sub, reduction = "umap", group.by = "db.scds_hybrid_class")
#> Error in CellDimPlot(pancreas_sub, reduction = "umap", group.by = "db.scds_hybrid_class"): db.scds_hybrid_class is not in the meta.data of srt object.
FeatureDimPlot(pancreas_sub, reduction = "umap", features = "db.scds_hybrid_score")
#> Warning: db.scds_hybrid_score are not in the features of srt.
#> Error in FeatureDimPlot(pancreas_sub, reduction = "umap", features = "db.scds_hybrid_score"): There are no valid features present.