Perform comprehensive single cell QC

Source: R/runQC.R

A wrapper function to run several QC algorithms on a SingleCellExperiment object containing cells after empty droplets have been removed.

runCellQC(
  inSCE,
  algorithms = c("QCMetrics", "scDblFinder", "cxds", "bcds", "cxds_bcds_hybrid",
    "decontX"),
  sample = NULL,
  collectionName = NULL,
  geneSetList = NULL,
  geneSetListLocation = "rownames",
  geneSetCollection = NULL,
  useAssay = "counts",
  seed = 12345,
  paramsList = NULL
)

Arguments

inSCE

A SingleCellExperiment object.
algorithms

Character vector. Specify which QC algorithms to run. Available options are "QCMetrics", "scrublet", "doubletFinder", "scDblFinder", "cxds", "bcds", "cxds_bcds_hybrid", and "decontX".
sample

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

Character. Name of a GeneSetCollection obtained by using one of the importGeneSet* functions. Default NULL.
geneSetList

See runPerCellQC. Default NULL.
geneSetListLocation

See runPerCellQC. Default NULL.
geneSetCollection

See runPerCellQC. Default NULL.
useAssay

A string specifying which assay contains the count matrix for cells.
seed

Seed for the random number generator. Default 12345.
paramsList

A list containing parameters for QC functions. Default NULL.

Value

SingleCellExperiment object containing the outputs of the specified algorithms in the colData of inSCE.

Examples

data(scExample, package = "singleCellTK")
sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'")
if (FALSE) {
sce <- runCellQC(sce)
}