runCxds: Find doublets/multiplets using cxds.

In compbiomed/singleCellTK: Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

Find doublets/multiplets using cxds.

Description

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.

Usage

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"

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.

Value

A SingleCellExperiment object with cxds output appended to the colData slot. The columns include cxds_score and optionally cxds_call.

See Also

cxds, plotCxdsResults, runCellQC

Examples

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

compbiomed/singleCellTK documentation built on Feb. 10, 2024, 3:32 a.m.