Package: diagFDR
Title: Assessing False Discovery Rate Claims in Proteomics
Version: 0.2.1
Date: 2026-10-25
Authors@R: c(
    person("Quentin", "Giai Gianetto", email = "quentin.giaigianetto@pasteur.fr",
           role = c("aut", "cre"), comment = c(ORCID = "0000-0001-6815-2498")),
    person("Marie", "Chion", role = "ctb", comment = c(ORCID = "0000-0001-8956-8388")),
    person("Alexandre", "Godmer", role = "ctb", comment = c(ORCID = "0000-0002-5211-5796")),
    person("Thibaut", "Douché", role = "ctb", comment = c(ORCID = "0000-0001-8627-6726")),
    person("Mariette", "Matondo", role = "ctb", comment = c(ORCID = "0000-0003-3958-7710")))
Description: Provides scope, calibration and stability diagnostics to
        assess false discovery rate (FDR) claims in peptide and protein
        identification workflows based on target-decoy competition and
        related confidence measures. Includes the recomputed decoy
        ratio of the reported list, accepted decoy counts and local
        decoy support, the FDP-CV benchmark, threshold elasticity,
        posterior error probability (PEP) concordance with the decoys,
        equal-chance checks and p-value calibration, explicit
        target/decoy label-propagation rules for grouped units,
        picked-protein competition, external validation by entrapment
        (raw and size-corrected estimates, scope-discordant-set error
        rate), a ground-truth simulator of target-decoy competition,
        and an HTML report. Methods are described in Chion et al.
        (2026) <doi:10.64898/2026.04.16.718468>.
URL: https://github.com/Jacky11/diagFDR,
        https://www.biorxiv.org/content/10.64898/2026.04.16.718468
BugReports: https://github.com/Jacky11/diagFDR/issues
License: GPL-3
Encoding: UTF-8
RoxygenNote: 7.3.1
Depends: R (>= 4.2.0)
Imports: dplyr, tibble, ggplot2, purrr, rlang, readr, xml2, cp4p,
        tidyr, scales, data.table, stats, utils
Suggests: arrow, knitr, officer, rvg, testthat (>= 3.0.0), withr,
        rmarkdown, jsonlite
VignetteBuilder: knitr
Config/testthat/edition: 3
LazyData: true
NeedsCompilation: no
Config/pak/sysreqs: libcairo2-dev cmake libfontconfig1-dev
        libfreetype6-dev make libicu-dev libpng-dev libuv1-dev
        libxml2-dev libx11-dev zlib1g-dev
Repository: https://jacky11.r-universe.dev
Date/Publication: 2026-10-28 14:26:33 UTC
RemoteUrl: https://github.com/jacky11/diagfdr
RemoteRef: HEAD
RemoteSha: aba106639928e6ca62f74f362d6cfd1d0bca0f59
Packaged: 2026-10-29 21:01:20 UTC; root
Author: Quentin Giai Gianetto [aut, cre] (ORCID:
    <https://orcid.org/0000-0001-6815-2498>),
  Marie Chion [ctb] (ORCID: <https://orcid.org/0000-0001-8956-8388>),
  Alexandre Godmer [ctb] (ORCID: <https://orcid.org/0000-0002-5211-5796>),
  Thibaut Douché [ctb] (ORCID: <https://orcid.org/0000-0001-8627-6726>),
  Mariette Matondo [ctb] (ORCID: <https://orcid.org/0000-0003-3958-7710>)
Maintainer: Quentin Giai Gianetto <quentin.giaigianetto@pasteur.fr>