Run doublet-calling with Scrublet — db

This function performs doublet-calling using the scrublet(python) package on a Seurat object.

Usage

db_Scrublet(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 scrublet.Scrublet function.

Examples

data("pancreas_sub")
pancreas_sub <- db_Scrublet(pancreas_sub)
#> 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.Scrublet_class")
#> Error in CellDimPlot(pancreas_sub, reduction = "umap", group.by = "db.Scrublet_class"): db.Scrublet_class is not in the meta.data of srt object.
FeatureDimPlot(pancreas_sub, reduction = "umap", features = "db.Scrublet_score")
#> Warning: db.Scrublet_score are not in the features of srt.
#> Error in FeatureDimPlot(pancreas_sub, reduction = "umap", features = "db.Scrublet_score"): There are no valid features present.