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
Packaged: 2026-10-28 14:47:10 UTC; qgiaigia
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>
Repository: CRAN
Date/Publication: 2026-10-28 15:20:02 UTC
Built: R 4.7.0; ; 2026-10-29 11:32:17 UTC; windows
