% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/dropletUtils_barcodeRank.R
 \name{runBarcodeRankDrops}
 \alias{runBarcodeRankDrops}
 \title{Identify empty droplets using \link[DropletUtils]{barcodeRanks}.}
 \usage{

 runBarcodeRankDrops(
   inSCE,
   sample = NULL,
   useAssay = "counts",
   lower = 100,

   fitBounds = NULL,

   df = 20
 )

 }
 \arguments{

 \item{inSCE}{A \linkS4class{SingleCellExperiment} object. Must contain a raw 
 counts matrix before empty droplets have been removed.}

 \item{sample}{Character vector or colData variable name. Indicates which 
 sample each cell belongs to. Default \code{NULL}.}

 \item{useAssay}{A string specifying which assay in the SCE to use. Default 
 \code{"counts"}}

 \item{lower}{See \link[DropletUtils]{barcodeRanks} for more information. 
 Default \code{100}.}

 \item{fitBounds}{See \link[DropletUtils]{barcodeRanks} for more information. 
 Default \code{NULL}.}

 \item{df}{See \link[DropletUtils]{barcodeRanks} for more information. Default 
 \code{20}.}

 }
 \value{

 A \linkS4class{SingleCellExperiment} object with the
 \link[DropletUtils]{barcodeRanks} output table appended to the
 \link{colData} slot. The columns include
 \code{dropletUtils_BarcodeRank_Knee} and 
 \code{dropletUtils_barcodeRank_inflection}. Please refer to the documentation
 of \link[DropletUtils]{barcodeRanks} for details.

 }
 \description{
 Run \link[DropletUtils]{barcodeRanks} on a count matrix

 provided in a \linkS4class{SingleCellExperiment} object. Distinguish between 
 droplets containing cells and ambient RNA in a droplet-based single-cell RNA 
 sequencing experiment.

 }
 \examples{

 data(scExample, package = "singleCellTK")
 sce <- runBarcodeRankDrops(inSCE = sce)

 }

 \seealso{
 \code{\link[DropletUtils]{barcodeRanks}}, 
 \code{\link{runDropletQC}}, \code{\link{plotBarcodeRankDropsResults}}
 }