Package: qch
Title: Query Composite Hypotheses
Version: 2.1.3
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, Rcpp, stats, stringr,
        utils
LinkingTo: Rcpp, RcppArmadillo
biocViews:
Encoding: UTF-8
LazyData: true
NeedsCompilation: yes
Packaged: 2026-07-03 19:26:48 UTC; root
RoxygenNote: 7.3.3
Config/pak/sysreqs: libgsl0-dev libicu-dev
Repository: https://tmaryhuard.r-universe.dev
Date/Publication: 2026-05-27 16:48:21 UTC
RemoteUrl: https://github.com/cran/qch
RemoteRef: HEAD
RemoteSha: a83f980907989f947612e01086f40bb220abc87d