Estimate numbers of detected genes, significantly differentially expressed genes, and median significant effect size

downSampleDepth(
  originalData,
  useAssay = "counts",
  minCount = 10,
  minCells = 3,
  maxDepth = 1e+07,
  realLabels,
  depthResolution = 10,
  iterations = 10
)

Arguments

originalData: SingleCellExperiment object storing all assay data from the shiny app.
useAssay: Character. The name of the assay to be used for subsampling.
minCount: Numeric. The minimum number of reads found for a gene to be considered detected.
minCells: Numeric. The minimum number of cells a gene must have at least 1 read in for it to be considered detected.
maxDepth: Numeric. The highest number of total reads to be simulated.
realLabels: Character. The name of the condition of interest. Must match a name from sample data.
depthResolution: Numeric. How many different read depth should the script simulate? Will simulate a number of experimental designs ranging from 10 reads to maxReadDepth, with logarithmic spacing.
iterations: Numeric. How many times should each experimental design be simulated?

Value

A 3-dimensional array, with dimensions = c(iterations, depthResolution, 3). [,,1] contains the number of detected genes in each simulated dataset, [,,2] contains the number of significantly differentially expressed genes in each simulation, and [,,3] contains the mediansignificant effect size in each simulation. If no genes are significantly differentially expressed, the median effect size defaults to infinity.

Examples

data("mouseBrainSubsetSCE")
subset <- mouseBrainSubsetSCE[seq(1000),]
res <- downSampleDepth(subset,
                       realLabels = "level1class",
                       iterations=2)
#> Warning: no non-missing arguments to min; returning Inf
#> Warning: no non-missing arguments to min; returning Inf
#> Warning: no non-missing arguments to min; returning Inf
#> Warning: no non-missing arguments to min; returning Inf
#> Warning: no non-missing arguments to min; returning Inf
#> Warning: no non-missing arguments to min; returning Inf
#> Warning: no non-missing arguments to min; returning Inf
#> Warning: no non-missing arguments to min; returning Inf