runDropletQC {singleCellTK} | R Documentation

## Perform comprehensive droplet QC

### Description

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

### Usage

    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")
    ## Not run:
    sce <- runDropletQC(sce)

    ## End(Not run)

[Package singleCellTK version 2.0.0 Index]