Confounding explorer — ConfoundingExplorer • ConfoundingExplorer

Confounding explorer

ConfoundingExplorer(
  sampleSizes = matrix(rep(5, 4), nrow = 2, dimnames = list(c("group1", "group2"),
    c("batch1", "batch2"))),
  fracVarCond = 0.25,
  fracVarBatch = 0.5,
  fracVarUnknown = 0,
  condEffectSize = 3,
  batchEffectSize = 3,
  unknownEffectSize = 0,
  unknownEffectType = "categorical",
  analysisApproach = "dontAdjust",
  seed = 123,
  addStopButton = TRUE
)

Arguments

sampleSizes: 2x2 numeric matrix giving the number of samples in each group. Row names must be c('group1', 'group2') and column names must be c('batch1', 'batch2').
fracVarCond, fracVarBatch, fracVarUnknown: Numeric scalars between 0 and 1. The fraction of variables affected by the condition effect, batch effect, and 'unknown' effect, respectively.
condEffectSize, batchEffectSize, unknownEffectSize: Numeric scalars. The condition, batch and 'unknown' effect size, respectively.
unknownEffectType: Character scalar, either 'categorical' or 'continuous', representing the type of 'unknown' effect to add.
analysisApproach: Character scalar. One of 'dontAdjust', 'inclBatch', 'removeBatch', 'removeBatchAccCond'. Determines what model is fit to the data.
seed: Numeric scalar, the random seed to use when simulating data.
addStopButton: Logical scalar. If TRUE (default), will add a button to stop the app (by calling shiny::stopApp).

Value

A shinyApp object

Author

Charlotte Soneson

Examples

if (interactive()) {
  ConfoundingExplorer()
}