runCellQC {singleCellTK} | R Documentation

## Perform comprehensive single cell QC

### Description

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

### Usage

    runCellQC(
      inSCE,
      algorithms = c("QCMetrics", "doubletCells", "cxds", "bcds", "cxds_bcds_hybrid",
        "scrublet", "doubletFinder", "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", "doubletCells", "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'")
    ## Not run:
    sce <- runCellQC(sce)

    ## End(Not run)

[Package singleCellTK version 2.0.0 Index]