runEmptyDrops {singleCellTK} | R Documentation

## Identify empty droplets using emptyDrops.

### Description

Run emptyDrops on the count matrix in the provided SingleCellExperiment object. Distinguish between droplets containing cells and ambient RNA in a droplet-based single-cell RNA sequencing experiment.

### Usage

    runEmptyDrops(
      inSCE,
      sample = NULL,
      useAssay = "counts",
      lower = 100,
      niters = 10000,
      testAmbient = FALSE,
      ignore = NULL,
      alpha = NULL,
      retain = NULL,
      barcodeArgs = list(),
      BPPARAM = BiocParallel::SerialParam()
    )

### Arguments

`inSCE` | Input SingleCellExperiment object. Must contain a raw counts matrix before empty droplets have been removed.
`sample` | Character vector. Indicates which sample each cell belongs to. emptyDrops will be run on cells from each sample separately. If NULL, then all cells will be processed together. Default NULL.
`useAssay` | A string specifying which assay in the SCE to use.
`lower` | See emptyDrops for more information.
`niters` | See emptyDrops for more information.
`testAmbient` | See emptyDrops for more information.
`ignore` | See emptyDrops for more information.
`alpha` | See emptyDrops for more information.
`retain` | See emptyDrops for more information.
`barcodeArgs` | See emptyDrops for more information.
`BPPARAM` | See emptyDrops for more information.

### Value

A SingleCellExperiment object with the emptyDrops output table appended to the colData slot. The columns include emptyDrops_total, emptyDrops_logprob, emptyDrops_pvalue, emptyDrops_limited, emptyDrops_fdr. Please refer to the documentation of emptyDrops for details.

### Examples

    # The following unfiltered PBMC_1k_v3 data were downloaded from
    # https://support.10xgenomics.com/single-cell-gene-expression/datasets/3.0.0
    # /pbmc_1k_v3
    # Only the top 10 cells with most counts and the last 10 cells with non-zero
    # counts are included in this example.
    # This example only serves as an proof of concept and a tutorial on how to
    # run the function. The results should not be
    # used for drawing scientific conclusions.
    data(scExample, package = "singleCellTK")
    sce <- runEmptyDrops(inSCE = sce)

[Package singleCellTK version 2.0.0 Index]