db_scds: Run doublet-calling with scds

In zh542370159/SCP: Single Cell Pipeline

Run doublet-calling with scds

Description

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")
CellDimPlot(pancreas_sub, reduction = "umap", group.by = "db.scds_hybrid_class")
FeatureDimPlot(pancreas_sub, reduction = "umap", features = "db.scds_hybrid_score")

zh542370159/SCP documentation built on Nov. 22, 2023, 2:34 a.m.