plotMASTThresholdGenes {singleCellTK} | R Documentation

## MAST Identify adaptive thresholds

### Description

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

### Usage

    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)

[Package singleCellTK version 2.2.0 Index]