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% Generated by roxygen2: do not edit by hand
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% Please edit documentation in R/dropletUtils_emptyDrops.R
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\name{runEmptyDrops}
\alias{runEmptyDrops}
\title{Identify empty droplets using \link[DropletUtils]{emptyDrops}.}
\usage{
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runEmptyDrops(
inSCE,
sample = NULL,
useAssay = "counts",
lower = 100,
niters = 10000,
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testAmbient = FALSE,
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ignore = NULL,
alpha = NULL,
retain = NULL,
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barcodeArgs = list(),
BPPARAM = BiocParallel::SerialParam()
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)
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}
\arguments{
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\item{inSCE}{A \linkS4class{SingleCellExperiment} object. Must contain a raw
counts matrix before empty droplets have been removed.}
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\item{sample}{Character vector or colData variable name. Indicates which
sample each cell belongs to. Default \code{NULL}.}
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\item{useAssay}{A string specifying which assay in the SCE to use. Default
\code{"counts"}}
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\item{lower}{See \link[DropletUtils]{emptyDrops} for more information.
Default \code{100}.}
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\item{niters}{See \link[DropletUtils]{emptyDrops} for more information.
Default \code{10000}.}
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\item{testAmbient}{See \link[DropletUtils]{emptyDrops} for more information.
Default \code{FALSE}.}
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\item{ignore}{See \link[DropletUtils]{emptyDrops} for more information.
Default \code{NULL}.}
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\item{alpha}{See \link[DropletUtils]{emptyDrops} for more information.
Default \code{NULL}.}
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\item{retain}{See \link[DropletUtils]{emptyDrops} for more information.
Default \code{NULL}.}
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\item{barcodeArgs}{See \link[DropletUtils]{emptyDrops} for more information.
Default \code{list()}.}
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\item{BPPARAM}{See \link[DropletUtils]{emptyDrops} for more information.
Default \code{BiocParallel::SerialParam()}.}
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}
\value{
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A \linkS4class{SingleCellExperiment} object with the
\link[DropletUtils]{emptyDrops} output table appended to the
\link{colData} slot. The columns include
\code{emptyDrops_total}, \code{emptyDrops_logprob},
\code{emptyDrops_pvalue}, \code{emptyDrops_limited}, \code{emptyDrops_fdr}.
Please refer to the documentation of \link[DropletUtils]{emptyDrops} for
details.
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}
\description{
Run \link[DropletUtils]{emptyDrops} on the count matrix in the
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provided \linkS4class{SingleCellExperiment} object.
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Distinguish between droplets containing cells and ambient RNA in a
droplet-based single-cell RNA sequencing experiment.
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}
\examples{
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data(scExample, package = "singleCellTK")
sce <- runEmptyDrops(inSCE = sce)
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}
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\seealso{
\code{\link{runDropletQC}}, \code{\link{plotEmptyDropsResults}},
\code{\link{plotEmptyDropsScatter}}
}
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