Find doublets/multiplets using cxds.

A wrapper function for cxds. Annotate doublets/multiplets using co-expression based approach. Generate a doublet score for each cell. Infer doublets if estNdbl is TRUE.

runCxds(
  inSCE,
  sample = NULL,
  seed = 12345,
  ntop = 500,
  binThresh = 0,
  verb = FALSE,
  retRes = FALSE,
  estNdbl = FALSE,
  useAssay = "counts"
)

Arguments

inSCE

A SingleCellExperiment object.

sample

Character vector or colData variable name. Indicates which sample each cell belongs to. Default NULL.

seed

Seed for the random number generator, can be NULL. Default 12345.

ntop

See cxds for more information. Default 500.

binThresh

See cxds for more information. Default 0.

verb

See cxds for more information. Default FALSE.

retRes

See cxds for more information. Default FALSE.

estNdbl

See cxds for more information. Default FALSE.

useAssay

A string specifying which assay in the SCE to use. Default "counts"

Value

A SingleCellExperiment object with cxds

output appended to the colData slot. The columns include cxds_score and optionally cxds_call.

Details

When the argument sample is specified, cxds will be run on cells from each sample separately. If sample = NULL, then all cells will be processed together.

See also

cxds, plotCxdsResults, runCellQC

Examples

data(scExample, package = "singleCellTK")
sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'")
sce <- runCxds(sce)
#> Sat Mar 18 10:30:30 2023 ... Running 'cxds'