plotMASTThresholdGenes: MAST Identify adaptive thresholds

In compbiomed/singleCellTK: Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

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)

compbiomed/singleCellTK documentation built on Oct. 27, 2024, 3:26 a.m.