multAdjust: Multiple testing adjustment

In stefpeschel/NetCoMi: Network Construction and Comparison for Microbiome Data

Multiple testing adjustment

Description

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

Usage

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

Arguments

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.

References

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

stefpeschel/NetCoMi documentation built on June 14, 2025, 1:15 p.m.