hommel {hommel}

Calculates adjusted p-values of Hommel's method efficiently.

Description

Calculates adjusted p-values of Hommel's method efficiently.

Usage

 hommel (p, simes = TRUE) 

Arguments

p

A vector of p-values.

simes

If TRUE, the Simes test is used (Hommel's method), if FALSE Hommel's robust test is used.

Value

Returns a hommel-class object.

Author(s)

Jelle Goeman, Rosa Meijer, Thijmen Krebs.

References

Hommel, G. (1988). A stagewise rejective multiple test procedure based on a modified Bonferroni test. Biometrika, 75(2), 383-386.

Meijer, R. J., Krebs, T. J., & Goeman, J. J. (2019). Hommel's procedure in linear time. Biometrical Journal, 61(1), 73-82.

Goeman, J., Meijer, R., Krebs, T., & Solari, A. (2016). Simultaneous control of all false discovery proportions in large-scale multiple hypothesis testing. arXiv preprint arXiv:1611.06739.

Examples

  #Generate a vector of pvalues
  set.seed(102)
  m <- 10
  pvalues <- c(runif(0.5*m,0,0.02), runif(0.5*m,0,1))
  
  # First step: create a hommel object.
  # Use Simes'test (simes = TRUE) or Hommel's robust test (simes = FALSE)
  hom <- hommel(pvalues, simes = TRUE)

  hom
  summary(hom)
  
  # retrieve familywise error adjusted p-values
  p.adjust(hom)
  
  # Find lower confidence bounds 
  # for the number of false null hypotheses (discoveries)
  # In any subset of interest
  discoveries(hom, 1:2)