qch: Query Composite Hypotheses

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) <doi:10.1093/bioinformatics/btab592> and De Walsche et al.(2023) <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.

Version: 2.0.0
Depends: R (≥ 2.10)
Imports: copula, dplyr, graphics, ks, purrr, qvalue, Rcpp, stats, stringr, utils
LinkingTo: Rcpp, RcppArmadillo
Published: 2024-03-29
Author: Tristan Mary-Huard ORCID iD [aut, cre], Annaig De Walsche ORCID iD [aut], Franck Gauthier ORCID iD [ctb]
Maintainer: Tristan Mary-Huard <tristan.mary-huard at agroparistech.fr>
License: GPL-3
NeedsCompilation: yes
CRAN checks: qch results

Documentation:

Reference manual: qch.pdf

Downloads:

Package source: qch_2.0.0.tar.gz
Windows binaries: r-devel: qch_2.0.0.zip, r-release: qch_2.0.0.zip, r-oldrel: qch_2.0.0.zip
macOS binaries: r-release (arm64): qch_2.0.0.tgz, r-oldrel (arm64): qch_2.0.0.tgz, r-release (x86_64): qch_2.0.0.tgz
Old sources: qch archive

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