Find doublets/multiplets using cxds. — runCxds • singleCellTK

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. Needs counts in assays slot.
sample: Character vector. Indicates which sample each cell belongs to. cxds will be run on cells from each sample separately. If NULL, then all cells will be processed together. Default NULL.
seed: Seed for the random number generator. 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.

Value

A SingleCellExperiment object with cxds output appended to the colData slot. The columns include cxds_score and optionally cxds_call. Please refer to the documentation of cxds for details.

Examples

data(scExample, package = "singleCellTK")
sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'")
sce <- runCxds(sce)
#> Thu Apr 28 11:27:45 2022 ... Running 'cxds'