Perform comprehensive droplet QC — runDropletQC • singleCellTK

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.

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

of inSCE.

data(scExample, package = "singleCellTK")
if (FALSE) {
sce <- runDropletQC(sce)
}