runBarcodeRankDrops {singleCellTK} | R Documentation

## Identify empty droplets using barcodeRanks.

### Description

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

### Usage

    runBarcodeRankDrops(
      inSCE,
      sample = NULL,
      useAssay = "counts",
      lower = 100,
      fitBounds = NULL,
      df = 20
    )

### Arguments

`inSCE` | A 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. Default `100`.
`fitBounds` | See emptyDrops for more information. Default `NULL`.
`df` | See emptyDrops for more information. Default `20`.

### Value

A SingleCellExperiment object with the barcodeRanks output table appended to the colData slot. The columns include dropletUtils_BarcodeRank_Knee and dropletUtils_BarcodeRank_Knee Please refer to the documentation of barcodeRanks 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 tutoriol on how to
    # run the function. The results should not be
    # used for drawing scientific conclusions.
    data(scExample, package = "singleCellTK")
    sce <- runBarcodeRankDrops(inSCE = sce)

[Package singleCellTK version 2.0.0 Index]