MAST Identify adaptive thresholds

Calculate and produce a list of thresholded counts (on natural scale), thresholds, bins, densities estimated on each bin, and the original data from thresholdSCRNACountMatrix

plotMASTThresholdGenes(
  inSCE,
  useAssay = "logcounts",
  doPlot = TRUE,
  isLogged = TRUE,
  check_sanity = TRUE
)

Arguments

inSCE

SingleCellExperiment object

useAssay

character, default "logcounts"

doPlot

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

isLogged

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

check_sanity

Logical scalar. Whether to perform MAST's sanity check to see if the counts are logged. Default TRUE

Value

Plot the thresholding onto the plotting region if plot == TRUE

or a graphical object if plot == FALSE.

Examples

data("mouseBrainSubsetSCE")
plotMASTThresholdGenes(mouseBrainSubsetSCE)
#> `fData` has no primerid.  I'll make something up.
#> `cData` has no wellKey.  I'll make something up.
#> Assuming data assay in position 1, with name et is log-transformed.
#> Warning: calling par(new=TRUE) with no plot