Perform comprehensive droplet QC

Source: R/runQC.R

A wrapper function to run several QC algorithms for determining empty droplets in single cell RNA-seq data

runDropletQC(
  inSCE,
  algorithms = c("QCMetrics", "emptyDrops", "barcodeRanks"),
  sample = NULL,
  useAssay = "counts",
  paramsList = NULL
)

Arguments

inSCE

A SingleCellExperiment object containing the full droplet count matrix
algorithms

Character vector. Specify which QC algorithms to run. Available options are "emptyDrops" and "barcodeRanks".
sample

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

A string specifying which assay contains the count matrix for droplets.
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")
if (FALSE) {
sce <- runDropletQC(sce)
}