% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/plotDEAnalysis.R
 \name{plotMASTThresholdGenes}
 \alias{plotMASTThresholdGenes}
 \title{MAST Identify adaptive thresholds}
 \usage{

 plotMASTThresholdGenes(
   inSCE,
   useAssay = "logcounts",

   doPlot = TRUE,

   isLogged = TRUE,
   check_sanity = TRUE
 )

 }
 \arguments{
 \item{inSCE}{SingleCellExperiment object}
 
 \item{useAssay}{character, default \code{"logcounts"}}
 

 \item{doPlot}{Logical scalar. Whether to directly plot in the plotting area.
 If \code{FALSE}, will return a graphical object which can be visualized with
 \code{grid.draw()}. Default \code{TRUE}.}
 

 \item{isLogged}{Logical scalar. Whether the assay used for the analysis is
 logged. If not, will do a \code{log(assay + 1)} transformation. Default
 \code{TRUE}.}
 

 \item{check_sanity}{Logical scalar. Whether to perform MAST's sanity check
 to see if the counts are logged. Default \code{TRUE}}
 }
 \value{

 Plot the thresholding onto the plotting region if \code{plot == TRUE}
 or a graphical object if \code{plot == FALSE}.

 }
 \description{
 Calculate and produce a list of thresholded counts (on natural scale),
 thresholds, bins, densities estimated on each bin, and the original data from
 \code{\link[MAST]{thresholdSCRNACountMatrix}}
 }
 \examples{
 data("mouseBrainSubsetSCE")

 plotMASTThresholdGenes(mouseBrainSubsetSCE)

 }