qch-package: qch: Query Composite Hypotheses

In qch: Query Composite Hypotheses

qch: Query Composite Hypotheses

Description

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) \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1093/bioinformatics/btab592")} and De Walsche et al.(2023) \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1101/2024.03.17.585412")}. 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.

Details

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

Author(s)

Maintainer: Tristan Mary-Huard [e-mail] (ORCID)

Authors:

• Annaig De Walsche [e-mail] (ORCID)

Other contributors:

• Franck Gauthier [e-mail] (ORCID) [contributor]

qch documentation built on May 29, 2024, 8:11 a.m.