`DownsampleCells.Rd`

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

DownsampleCells(originalData, useAssay = "counts", minCountDetec = 10, minCellsDetec = 3, minCellnum = 10, maxCellnum = 1000, realLabels, depthResolution = 10, iterations = 10, totalReads = 1e+06)

originalData | SCtkExperiment. The SCtkExperiment object storing all assay data from the shiny app. |
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useAssay | Character. The name of the assay to be used for subsampling. |

minCountDetec | Numeric. The minimum number of reads found for a gene to be considered detected. |

minCellsDetec | Numeric. The minimum number of cells a gene must have at least 1 read in for it to be considered detected. |

minCellnum | Numeric. The minimum number of virtual cells to include in the smallest simulated dataset. |

maxCellnum | Numeric. The maximum number of virtual cells to include in the largest simulated dataset |

realLabels | Character. The name of the condition of interest. Must match a name from sample data. If only two factors present in the corresponding colData, will default to t-test. If multiple factors, will default to ANOVA. |

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? |

totalReads | Numeric. How many aligned reads to put in each simulated dataset. |

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.

data("mouseBrainSubsetSCE") subset <- mouseBrainSubsetSCE[1:1000,] res <- DownsampleCells(subset, realLabels = "level1class", iterations=2)