Run doublet-calling with scDblFinder — db_scDblFinder • scop

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

Usage

db_scDblFinder(srt, assay = "RNA", db_rate = ncol(srt)/1000 * 0.01, ...)

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.
...: Additional arguments to be passed to scDblFinder::scDblFinder function.

Examples

data("pancreas_sub")
pancreas_sub <- db_scDblFinder(pancreas_sub)
CellDimPlot(
  srt = pancreas_sub,
  reduction = "umap",
  group.by = "db.scDblFinder_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.scDblFinder_score"
)