runEmptyDrops: Identify empty droplets using emptyDrops.

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

Identify empty droplets using emptyDrops.

Description

Run emptyDrops on the count matrix in the provided SingleCellExperiment object. Distinguish between droplets containing cells and ambient RNA in a droplet-based single-cell RNA sequencing experiment.

Usage

runEmptyDrops(
  inSCE,
  sample = NULL,
  useAssay = "counts",
  lower = 100,
  niters = 10000,
  testAmbient = FALSE,
  ignore = NULL,
  alpha = NULL,
  retain = NULL,
  barcodeArgs = list(),
  BPPARAM = BiocParallel::SerialParam()
)

Arguments

inSCE	A SingleCellExperiment object. Must contain a raw counts matrix before empty droplets have been removed.
sample	Character vector or colData variable name. Indicates which sample each cell belongs to. Default NULL.
useAssay	A string specifying which assay in the SCE to use. Default "counts"
lower	See emptyDrops for more information. Default 100.
niters	See emptyDrops for more information. Default 10000.
testAmbient	See emptyDrops for more information. Default FALSE.
ignore	See emptyDrops for more information. Default NULL.
alpha	See emptyDrops for more information. Default NULL.
retain	See emptyDrops for more information. Default NULL.
barcodeArgs	See emptyDrops for more information. Default list().
BPPARAM	See emptyDrops for more information. Default BiocParallel::SerialParam().

Value

A SingleCellExperiment object with the emptyDrops output table appended to the colData slot. The columns include emptyDrops_total, emptyDrops_logprob, emptyDrops_pvalue, emptyDrops_limited, emptyDrops_fdr. Please refer to the documentation of emptyDrops for details.

See Also

runDropletQC, plotEmptyDropsResults, plotEmptyDropsScatter

Examples

data(scExample, package = "singleCellTK")
sce <- runEmptyDrops(inSCE = sce)

compbiomed/singleCellTK documentation built on June 11, 2025, 9:45 a.m.