runDoubletCells: Detect doublet cells using scDblFinder.

Description Usage Arguments Details Value References See Also Examples

View source: R/scran_doubletCells.R

Description

A wrapper function for scDblFinder. Identify potential doublet cells based on simulations of putative doublet expression profiles. Generate a doublet score for each cell.

Usage

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runDoubletCells(
  inSCE,
  sample = NULL,
  useAssay = "counts",
  nNeighbors = 50,
  simDoublets = max(10000, ncol(inSCE)),
  seed = 12345,
  BPPARAM = BiocParallel::SerialParam()
)

Arguments

inSCE

A SingleCellExperiment object.

sample

Character vector. Indicates which sample each cell belongs to. scDblFinder will be run on cells from each sample separately.

useAssay

A string specifying which assay in the SCE to use.

nNeighbors

Number of nearest neighbors used to calculate density for doublet detection. Default 50.

simDoublets

Number of simulated doublets created for doublet detection. Default 10000.

seed

Seed for the random number generator. Default 12345.

BPPARAM

A BiocParallelParam object specifying whether the neighbour searches should be parallelized.

Details

This function is a wrapper function for scDblFinder. runDoubletCells runs scDblFinder for each sample within inSCE iteratively. The resulting doublet scores for all cells will be appended to the colData of inSCE.

Value

A SingleCellExperiment object with the 'scran_doubletCells_score' column added to the colData slot.

References

Lun ATL (2018). Detecting doublet cells with scran. https://ltla.github.io/SingleCellThoughts/software/doublet_detection/bycell.html

See Also

doubletCells

Examples

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data(scExample, package = "singleCellTK")
sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'")
sce <- runDoubletCells(sce)

singleCellTK documentation built on Nov. 8, 2020, 5:21 p.m.