% Generated by roxygen2: do not edit by hand

 % Please edit documentation in R/scDblFinder_doubletDetection.R
 \name{runScDblFinder}
 \alias{runScDblFinder}

 \title{Detect doublet cells using \link[scDblFinder]{scDblFinder}.}

 \usage{

 runScDblFinder(

   inSCE,
   sample = NULL,
   useAssay = "counts",
   nNeighbors = 50,

   simDoublets = max(10000, ncol(inSCE)),

   seed = 12345,

   BPPARAM = BiocParallel::SerialParam(RNGseed = seed)

 )

 }
 \arguments{

 \item{inSCE}{A \linkS4class{SingleCellExperiment} object.}

 \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{nNeighbors}{Number of nearest neighbors used to calculate density for

 doublet detection. Default \code{50}.}

 \item{simDoublets}{Number of simulated doublets created for doublet

 detection. Default \code{10000}.}

 \item{seed}{Seed for the random number generator, can be set to \code{NULL}.

 Default \code{12345}.}

 \item{BPPARAM}{A \code{\link[BiocParallel]{BiocParallelParam-class}} object
 specifying whether the neighbour searches should be parallelized. Default
 \code{BiocParallel::SerialParam(RNGseed = seed)}.}

 }
 \value{
 A \link[SingleCellExperiment]{SingleCellExperiment} object with the

 scDblFinder QC outputs added to the \link{colData} slot.

 }
 \description{

 A wrapper function for \link[scDblFinder]{scDblFinder}. Identify

  potential doublet cells based on simulations of putative doublet expression
  profiles. Generate a doublet score for each cell.
 }

 \details{

 This function is a wrapper function for
 \link[scDblFinder]{scDblFinder}. \code{runScDblFinder} runs
 \link[scDblFinder]{scDblFinder} for each sample within \code{inSCE}
 iteratively. The resulting doublet scores for all cells will be appended to

 the \code{\link{colData}} of \code{inSCE}.

 }

 \examples{

 data(scExample, package = "singleCellTK")

 sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'")

 sce <- runScDblFinder(sce)

 }
 \references{
 Lun ATL (2018). Detecting doublet cells with scran.

  \url{https://ltla.github.io/SingleCellThoughts/software/doublet_detection/bycell.html}

 }
 \seealso{

 \code{\link[scDblFinder]{scDblFinder}},

 \code{\link{plotScDblFinderResults}}, \code{\link{runCellQC}}

 }