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

In zh542370159/SCP: Single Cell Pipeline

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

Description

Identification of heterotypic (or neotypic) doublets in single-cell RNAseq data.

Usage

RunDoubletCalling(
  srt,
  assay = "RNA",
  db_method = "scDblFinder",
  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_method	Doublet-calling methods used. Can be one of scDblFinder, Scrublet, DoubletDetection, scds_cxds, scds_bcds, scds_hybrid
db_rate	The expected doublet rate. By default this is assumed to be 1% per thousand cells captured (so 4% among 4000 thousand cells), which is appropriate for 10x datasets.
...	Arguments passed to the corresponding doublet-calling method.

Value

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

Examples

data("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")

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