find_cells: Annotate a SingleCellExperiment with EmptyDrops predictions

In combiz/scFlow: A Single-Cell/Nuclei Analysis Toolkit

Annotate a SingleCellExperiment with EmptyDrops predictions

Description

Calculates the following QC metric:

• is_empty_drop - is the barcode an empty drop

Usage

find_cells(
  sce,
  lower = 100,
  retain = "auto",
  alpha_cutoff = 0.001,
  niters = 10000,
  expect_cells = 3000,
  ...
)

Arguments

sce	a SingleCellExperiment object
lower	see DropletUtils::emptyDrops()
retain	see DropletUtils::emptyDrops(). Use "auto" to calculate the parameter from the top expect_cells cells (cellranger method).
alpha_cutoff	The alpha cutoff used for Monte Carlo signficance.
niters	the number of Monte Carlo iterations
expect_cells	the number of cells expected for auto retain
...	additional arguments for uniformity testing

Value

sce a SingleCellExperiment object annotated with emptyDrops metrics

See Also

Other annotation functions: .preprocess_seurat_object(), annotate_celltype_metrics(), annotate_integrated_sce(), annotate_merged_sce(), annotate_sce(), annotate_sce_cells(), annotate_sce_genes(), filter_sce(), find_singlets(), generate_sce(), map_ensembl_gene_id(), merge_sce(), read_metadata(), report_celltype_metrics(), report_celltype_model(), report_merged_sce(), report_qc_sce(), run_doubletfinder(), sce_to_seu()

combiz/scFlow documentation built on Feb. 25, 2024, 10:25 a.m.