Run doublet-calling for single cell RNA-seq data.

Run doublet-calling for single cell RNA-seq data.

Usage

RunDoubletCalling(
  srt,
  assay = "RNA",
  db_rate = ncol(srt)/1000 * 0.01,
  db_method = "scDblFinder",
  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.

db_method

Method used for doublet-calling. Can be one of "scDblFinder", "Scrublet", "DoubletDetection", "scds_cxds", "scds_bcds", "scds_hybrid".

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 the corresponding doublet-calling method.

verbose

Whether to print the message. Default is TRUE.

Value

Returns a Seurat object with the doublet prediction results and prediction scores stored in the meta.data.

Examples

data(pancreas_sub)
pancreas_sub <- standard_scop(pancreas_sub)
pancreas_sub <- RunDoubletCalling(
  pancreas_sub,
  db_method = "scDblFinder"
)
CellDimPlot(
  pancreas_sub,
  reduction = "umap",
  group.by = "db.scDblFinder_class"
)

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