FWE: FWE Adjustment Using Closed Testing or Stepdown MinP
In NPC: Nonparametric Combination of Hypothesis Tests

Description Usage Arguments Value Note Author(s) References

This function adjusts a set of p-values to control the family-wise error rate (FWE). It does so using either closed testing (Marcus, Peritz, and Gabriel 1976) or the stepdown MinP algorithm (Westfall and Young 1993, 66–7). Because these methods take into account the dependence among the p-values, they are much less conservative than traditional FWE adjustments like the Bonferroni correction. Closed testing becomes very computationally intensive as the number of p-values increases.

1	FWE(PV, stepdown = TRUE, cfun = NULL)

`PV`	A matrix containing the permutation distribution of (pseudo) p-values. The first row should be the observed p-values and the remaining rows the permutation distribution.
`stepdown`	Use stepdown MinP to adjust p-values? (logical)
`cfun`	Combining function to be used for closed-testing adjustment (function)

A vector of adjusted p-values

Derived from the FWE.minP function (http://www.wiley.com/legacy/wileychi/pesarin/supp/R_functions.zip) provided by Pesarin and Salmaso (2010) and the closetest function (http://static.gest.unipd.it/~salmaso/web/clostest.r) provided by Basso et al. (2009).

Devin Caughey <devin.caughey@gmail.com>

Basso, Dario, Fortunato Pesarin, Luigi Salmaso, and Aldo Solar. 2009. Permutation Tests for Stochastic Ordering and ANOVA: Theory and Applications with R. London: Springer.

Marcus, Ruth, Eric Peritz, and K. R. Gabriel. 1976. “On Closed Testing Procedures with Special Reference to Ordered Analysis of Variance.” Biometrika 63 (3): 655-660.

Pesarin, Fortunato, and Luigi Salmaso. 2010. Permutation Tests for Complex Data. Chichester, UK: Wiley.

Westfall, P. H., and S. S. Young. 1993. Resampling-Based Multiple Testing: Examples and Methods for p-Value Adjustment. New York: Wiley.

NPC documentation built on May 2, 2019, 5:07 a.m.