Provides functions for the joint analysis of Q sets of p-values obtained for the same list of items. This joint analysis is performed by querying a composite hypothesis, i.e. an arbitrary complex combination of simple hypotheses, as described in Mary-Huard et al. (2021) tools:::Rd_expr_doi("10.1093/bioinformatics/btab592") and De Walsche et al.(2025) tools:::Rd_expr_doi(" 10.1093/nargab/lqaf118"). In this approach, the Q-uplet of p-values associated with each item is distributed as a multivariate mixture, where each of the 2^Q components corresponds to a specific combination of simple hypotheses. The dependence between the p-value series is considered using a Gaussian copula function. A p-value for the composite hypothesis test is derived from the posterior probabilities.
Maintainer: Tristan Mary-Huard tristan.mary-huard@agroparistech.fr (ORCID)
Authors:
Annaig De Walsche annaig.de-walsche@inrae.fr (ORCID)
Other contributors:
Franck Gauthier franck.gauthier@inrae.fr (ORCID) [contributor]
The main functions of the package GetHconfig, GetH1AtLeast,
GetH1Equal,
qch.fit and qch.test correspond to the
4 steps for querying a composite hypothesis:
Building all possible combination of simple hypotheses \(H_0\)/\(H_1\)
Composite alternative hypothesis formulation
Inferring the null distribution
Testing the composite null hypothesis