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Run Power Simulations for rescueSim Data

Source: R/runPowerAnalysis.R
runRescueSimPower.Rd

Simulate scRNA-seq data under different experimental settings and compute statistical power to detect differential expression (DE) using a user-specified DE function.

Usage

runRescueSimPower(
  baseParams,
  scenarios,
  deFunction,
  nSim = 1,
  padjThresh = 0.05,
  returnFDR = FALSE,
  conditions = NULL,
  saveSimPath = NULL,
  saveDePath = NULL,
  verbose = TRUE,
  ...
)

Arguments

baseParams

A RescueSimParams object containing baseline simulation parameters.

scenarios

A data.frame specifying simulation settings to vary. Column names must match slots in the RescueSimParams object. Each row defines one scenario.

deFunction

A function that takes a SingleCellExperiment object simulated using simRescueData and returns a data.frame with columns gene and padj.

nSim

Integer specifying the number of simulations to run per scenario. Default is 1.

padjThresh

Significance threshold to call DE (e.g., FDR < 0.05). Default is 0.05.

returnFDR

Logical. Whether to calculate and return the false discovery rate (FDR) along with power. Default is TRUE.

conditions

A character vector of length 2 specifying the conditions to compare (e.g., c("time1", "time3_group1")). If NULL (default), the comparison is inferred based on available conditions in rowData, comparing the baseline condition (e.g., "time0", "group0", or "time0_group0") to the final condition (e.g., last timepoint, or group 1 at the final timepoint).

saveSimPath

Optional path to directory where simulated SCE objects should be saved as .rds files. If NULL (default), simulated data is not saved.

saveDePath

Optional path to directory where DE result data.frames should be saved as .rds files. If NULL (default), results are not saved.

verbose

Logical. Whether to print progress messages. Default is TRUE.

...

Additional arguments passed to deFunction().

Value

A data.frame with one row per simulation replicate, including:

  • Power: proportion of truly DE genes detected

  • FDR: false discovery rate (if returnFDR = TRUE)

  • Scenario settings and simulation number

  • The reference and comparison condition used

Optionally, simulated datasets and DE results can be saved to disk.

Details

For each scenario, this function simulates nSim datasets based on the, supplied settings, applies the user-supplied DE method, and calculates power as the proportion of true DE genes correctly identified. DE status is determined by assessing equality in the simulated log2 fold-change values between conditions. False discovery rate (FDR) is optionally calculated as the proportion of genes called DE that are not truly DE.

See also

isDEbetweenConditions, simRescueData, updateRescueSimParams, RescueSimParams