Package: qch
Title: Query Composite Hypotheses
Version: 2.1.2
Authors@R: c(
    person("Tristan", "Mary-Huard", , "tristan.mary-huard@agroparistech.fr", role = c("aut", "cre"),
           comment = c(ORCID = "0000-0002-3839-9067")),
    person("Annaig", "De Walsche", , "annaig.de-walsche@inrae.fr", role = "aut",
           comment = c(ORCID = "0000-0003-0603-1716")),
    person("Franck", "Gauthier", , "franck.gauthier@inrae.fr", role = "ctb",
           comment = c(ORCID = "0000-0003-0574-065X"))
  )
Author: Tristan Mary-Huard [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-3839-9067>),
  Annaig De Walsche [aut] (ORCID:
    <https://orcid.org/0000-0003-0603-1716>),
  Franck Gauthier [ctb] (ORCID: <https://orcid.org/0000-0003-0574-065X>)
Maintainer: Tristan Mary-Huard <tristan.mary-huard@agroparistech.fr>
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) <doi:10.1093/bioinformatics/btab592> and De Walsche et
    al.(2025) <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.
License: GPL-3
Depends: R (>= 2.10)
Imports: copula, dplyr, graphics, ks, purrr, qvalue, Rcpp, stats,
        stringr, utils
LinkingTo: Rcpp, RcppArmadillo
biocViews:
Encoding: UTF-8
LazyData: true
NeedsCompilation: yes
Packaged: 2026-02-16 12:11:58 UTC; adewalsc
RoxygenNote: 7.3.3
Repository: CRAN
Date/Publication: 2026-02-16 13:20:02 UTC
Built: R 4.6.0; x86_64-apple-darwin20; 2026-04-25 20:45:59 UTC; unix
Archs: qch.so.dSYM
