Multiple testing adjustment — multAdjust • NetCoMi

The functions adjusts a vector of p-values for multiple testing

Usage

multAdjust(
  pvals,
  adjust = "adaptBH",
  trueNullMethod = "convest",
  pTrueNull = NULL,
  verbose = FALSE
)

pvals: numeric vector with p-values
adjust: character specifying the method used for adjustment. Can be "lfdr", "adaptBH", or one of the methods provided by p.adjust.
trueNullMethod: character indicating the method used for estimating the proportion of true null hypotheses from a vector of p-values. Used for the adaptive Benjamini-Hochberg method for multiple testing adjustment (chosen by adjust = "adaptBH"). Accepts the provided options of the method argument of propTrueNull: "convest"(default), "lfdr", "mean", and "hist". Can alternatively be "farco" for the "iterative plug-in method" proposed by Farcomeni (2007).
pTrueNull: proportion of true null hypothesis used for the adaptBH method. If NULL, the proportion is computed using the method defined via trueNullMethod.
verbose: if TRUE, progress messages are returned.

Farcomeni A (2007). “Some results on the control of the false discovery rate under dependence.” Scandinavian Journal of Statistics, 34(2), 275–297.