generateSimulatedData: Generates a single simulated dataset, bootstrapping from the...

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

Generates a single simulated dataset, bootstrapping from the input counts matrix.

Description

Generates a single simulated dataset, bootstrapping from the input counts matrix.

Usage

generateSimulatedData(totalReads, cells, originalData, realLabels)

Arguments

totalReads	Numeric. The total number of reads in the simulated dataset, to be split between all simulated cells.
cells	Numeric. The number of virtual cells to simulate.
originalData	Matrix. The original raw read count matrix. When used within the Shiny app, this will be assay(SCEsetObject, "counts").
realLabels	Factor. The condition labels for differential expression. If only two factors present, will default to t-test. If multiple factors, will default to ANOVA.

Value

A simulated counts matrix, the first row of which contains the 'true' labels for each virtual cell.

Examples

data("mouseBrainSubsetSCE")
res <- generateSimulatedData(
         totalReads = 1000, cells=10,
         originalData = assay(mouseBrainSubsetSCE, "counts"),
         realLabels = colData(mouseBrainSubsetSCE)[, "level1class"])

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