{
  "_id": "6a168ef5acfb0bcc41d77e9c",
  "Package": "diagFDR",
  "Title": "Verifiable FDR Diagnostics for Proteomics",
  "Version": "0.1.1",
  "Authors@R": "c(person(\"Quentin\", \"Giai Gianetto\", email = \"quentin.giaigianetto@pasteur.fr\", role = c(\"aut\", \"cre\")))",
  "Description": "Provides methods to compute verifiable false discovery\nrate (FDR) diagnostic checks for workflows based on\ntarget-decoy competition and related confidence measures.\nImplements calibration, stability and tail diagnostics,\nincluding tail support, threshold elasticity, posterior error\nprobability (PEP) reliability, and equal-chance checks. If you\nused this package in your research, please cite the associated\npreprint <doi:10.64898/2026.04.16.718468>. Detailed examples of\nusing this package can also be found on the GitHub repository\n(<https://github.com/Jacky11/diagFDR>).",
  "URL": "https://www.biorxiv.org/content/10.64898/2026.04.16.718468",
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  "Author": "Quentin Giai Gianetto [aut, cre]",
  "Maintainer": "Quentin Giai Gianetto <quentin.giaigianetto@pasteur.fr>",
  "Repository": "https://cran.r-universe.dev",
  "Date/Publication": "2026-04-27 20:36:28 UTC",
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  "_exports": [
    "as_dfdr_tbl",
    "dfdr_bh_diagnostics",
    "dfdr_bh_elasticity",
    "dfdr_curve_stability",
    "dfdr_elasticity",
    "dfdr_equal_chance_qbands",
    "dfdr_headline",
    "dfdr_local_tail",
    "dfdr_p_calibration",
    "dfdr_pep_decoy_sanity",
    "dfdr_pep_reliability",
    "dfdr_pep_reliability_tdc",
    "dfdr_pi0_storey",
    "dfdr_plot_bh_elasticity",
    "dfdr_plot_cv",
    "dfdr_plot_dalpha",
    "dfdr_plot_dwin",
    "dfdr_plot_elasticity",
    "dfdr_plot_equal_chance",
    "dfdr_plot_fdrhat_pi0",
    "dfdr_plot_p_calibration",
    "dfdr_plot_p_calibration2",
    "dfdr_plot_p_density_by_decoy",
    "dfdr_plot_pep_density_by_decoy",
    "dfdr_plot_pep_reliability",
    "dfdr_plot_pep_reliability_tdc",
    "dfdr_plot_pi0",
    "dfdr_plot_scope_disagreement_matrix",
    "dfdr_plot_score_distributions",
    "dfdr_render_report",
    "dfdr_run_all",
    "dfdr_run_jaccard",
    "dfdr_scope_disagreement",
    "dfdr_summary_headline",
    "dfdr_sumpep",
    "dfdr_write_manifest",
    "dfdr_write_readme",
    "dfdr_write_report",
    "diann_global_minrunq",
    "diann_global_precursor",
    "diann_runxprecursor",
    "flag_headline",
    "mokapot_competed_universe",
    "read_dfdr_maxquant_msms",
    "read_dfdr_mzid",
    "read_diann_parquet",
    "read_mokapot_psms",
    "read_spectronaut",
    "read_spectronaut_efficient",
    "score_to_pvalue",
    "spectronaut_runxprecursor"
  ],
  "_help": [
    {
      "page": "as_dfdr_tbl",
      "title": "Create a 'dfdr_tbl'",
      "topics": [
        "as_dfdr_tbl"
      ]
    },
    {
      "page": "dfdr_bh_diagnostics",
      "title": "BH diagnostics at a headline alpha (threshold, discoveries, boundary support)",
      "topics": [
        "dfdr_bh_diagnostics"
      ]
    },
    {
      "page": "dfdr_bh_elasticity",
      "title": "BH list elasticity (Jaccard) across alpha values",
      "topics": [
        "dfdr_bh_elasticity"
      ]
    },
    {
      "page": "dfdr_curve_stability",
      "title": "Stability curve across alpha values",
      "topics": [
        "dfdr_curve_stability"
      ]
    },
    {
      "page": "dfdr_elasticity",
      "title": "Threshold elasticity (list stability to cutoff perturbation)",
      "topics": [
        "dfdr_elasticity"
      ]
    },
    {
      "page": "dfdr_equal_chance_qbands",
      "title": "Equal-chance plausibility by q-value bands",
      "topics": [
        "dfdr_equal_chance_qbands"
      ]
    },
    {
      "page": "dfdr_headline",
      "title": "Headline stability diagnostics at a given alpha",
      "topics": [
        "dfdr_headline"
      ]
    },
    {
      "page": "dfdr_local_tail",
      "title": "Local tail support near the cutoff",
      "topics": [
        "dfdr_local_tail"
      ]
    },
    {
      "page": "dfdr_p_calibration",
      "title": "P-value calibration diagnostic (ECDF vs uniform; stratified)",
      "topics": [
        "dfdr_p_calibration"
      ]
    },
    {
      "page": "dfdr_pep_decoy_sanity",
      "title": "Decoy PEP sanity checks",
      "topics": [
        "dfdr_pep_decoy_sanity"
      ]
    },
    {
      "page": "dfdr_pep_reliability",
      "title": "Posterior Error Probability (PEP) reliability and internal PEP calibration error (IPE)",
      "topics": [
        "dfdr_pep_reliability"
      ]
    },
    {
      "page": "dfdr_pep_reliability_tdc",
      "title": "Target-focused PEP reliability using a TDC-style error proxy",
      "topics": [
        "dfdr_pep_reliability_tdc"
      ]
    },
    {
      "page": "dfdr_pi0_storey",
      "title": "Storey pi_0(lambda) tail-uniformity diagnostic",
      "topics": [
        "dfdr_pi0_storey"
      ]
    },
    {
      "page": "dfdr_plot_bh_elasticity",
      "title": "Plot BH elasticity (Jaccard) vs alpha",
      "topics": [
        "dfdr_plot_bh_elasticity"
      ]
    },
    {
      "page": "dfdr_plot_cv",
      "title": "Plot 'CV_hat' versus 'alpha'",
      "topics": [
        "dfdr_plot_cv"
      ]
    },
    {
      "page": "dfdr_plot_dalpha",
      "title": "Plot decoy support D_alpha versus 'alpha'",
      "topics": [
        "dfdr_plot_dalpha"
      ]
    },
    {
      "page": "dfdr_plot_dwin",
      "title": "Plot local decoy support 'D_alpha_win' versus 'alpha'",
      "topics": [
        "dfdr_plot_dwin"
      ]
    },
    {
      "page": "dfdr_plot_elasticity",
      "title": "Plot threshold elasticity (Jaccard) versus 'alpha'",
      "topics": [
        "dfdr_plot_elasticity"
      ]
    },
    {
      "page": "dfdr_plot_equal_chance",
      "title": "Plot equal-chance plausibility by q-value bands",
      "topics": [
        "dfdr_plot_equal_chance"
      ]
    },
    {
      "page": "dfdr_plot_fdrhat_pi0",
      "title": "Plot Storey-style estimated FDR curve: \\hatpi_0 m t / R(t)",
      "topics": [
        "dfdr_plot_fdrhat_pi0"
      ]
    },
    {
      "page": "dfdr_plot_p_calibration",
      "title": "Plot p-value calibration (ECDF minus uniform)",
      "topics": [
        "dfdr_plot_p_calibration"
      ]
    },
    {
      "page": "dfdr_plot_p_calibration2",
      "title": "P-value calibration plot (cp4p-style), with multiple pi0 reference curves",
      "topics": [
        "dfdr_plot_p_calibration2"
      ]
    },
    {
      "page": "dfdr_plot_p_density_by_decoy",
      "title": "Plot (pseudo-)p-value density by decoy/target",
      "topics": [
        "dfdr_plot_p_density_by_decoy"
      ]
    },
    {
      "page": "dfdr_plot_pep_density_by_decoy",
      "title": "Plot PEP density by decoy/target",
      "topics": [
        "dfdr_plot_pep_density_by_decoy"
      ]
    },
    {
      "page": "dfdr_plot_pep_reliability",
      "title": "Plot PEP reliability",
      "topics": [
        "dfdr_plot_pep_reliability"
      ]
    },
    {
      "page": "dfdr_plot_pep_reliability_tdc",
      "title": "Plot target-focused PEP reliability (TDC-style)",
      "topics": [
        "dfdr_plot_pep_reliability_tdc"
      ]
    },
    {
      "page": "dfdr_plot_pi0",
      "title": "Plot Storey pi_0(lambda) curve",
      "topics": [
        "dfdr_plot_pi0"
      ]
    },
    {
      "page": "dfdr_plot_scope_disagreement_matrix",
      "title": "Plot scope disagreement as a Jaccard overlap heatmap",
      "topics": [
        "dfdr_plot_scope_disagreement_matrix"
      ]
    },
    {
      "page": "dfdr_plot_score_distributions",
      "title": "Plot target vs decoy score distributions",
      "topics": [
        "dfdr_plot_score_distributions"
      ]
    },
    {
      "page": "dfdr_render_report",
      "title": "Render a human-readable HTML report from 'dfdr_run_all' output",
      "topics": [
        "dfdr_render_report"
      ]
    },
    {
      "page": "dfdr_run_all",
      "title": "Run a standard set of FDR QC diagnostics",
      "topics": [
        "dfdr_run_all"
      ]
    },
    {
      "page": "dfdr_run_jaccard",
      "title": "Inter-run Jaccard overlap matrix at a fixed threshold",
      "topics": [
        "dfdr_run_jaccard"
      ]
    },
    {
      "page": "dfdr_scope_disagreement",
      "title": "Scope disagreement between two lists",
      "topics": [
        "dfdr_scope_disagreement"
      ]
    },
    {
      "page": "dfdr_summary_headline",
      "title": "Build a headline summary table (one row per list)",
      "topics": [
        "dfdr_summary_headline"
      ]
    },
    {
      "page": "dfdr_sumpep",
      "title": "Expected number of false targets among accepted identifications",
      "topics": [
        "dfdr_sumpep"
      ]
    },
    {
      "page": "dfdr_write_manifest",
      "title": "Write a manifest file describing parameters, list metadata, and warnings",
      "topics": [
        "dfdr_write_manifest"
      ]
    },
    {
      "page": "dfdr_write_readme",
      "title": "Write a human-readable 'README.md' report",
      "topics": [
        "dfdr_write_readme"
      ]
    },
    {
      "page": "dfdr_write_report",
      "title": "Write diagnostic outputs to a folder",
      "topics": [
        "dfdr_write_report"
      ]
    },
    {
      "page": "diann_global_minrunq",
      "title": "DIA-NN: global precursor list built by minimum run-wise q across runs",
      "topics": [
        "diann_global_minrunq"
      ]
    },
    {
      "page": "diann_global_precursor",
      "title": "DIA-NN -> global precursor universe (deduplicated by 'Precursor.Id')",
      "topics": [
        "diann_global_precursor"
      ]
    },
    {
      "page": "diann_runxprecursor",
      "title": "DIA-NN -> run-by-precursor universe (deduplicated within run)",
      "topics": [
        "diann_runxprecursor"
      ]
    },
    {
      "page": "flag_headline",
      "title": "Flag diagnostic values based on heuristic thresholds",
      "topics": [
        "flag_headline"
      ]
    },
    {
      "page": "mokapot_competed_universe",
      "title": "Create a competed-winner universe from mokapot PSM outputs",
      "topics": [
        "mokapot_competed_universe"
      ]
    },
    {
      "page": "print.dfdr_tbl",
      "title": "Print a 'dfdr_tbl'",
      "topics": [
        "print.dfdr_tbl"
      ]
    },
    {
      "page": "read_dfdr_maxquant_msms",
      "title": "Read MaxQuant 'msms.txt' into a 'dfdr_tbl' (PSM-level; reconstructed TDC q-values)",
      "topics": [
        "read_dfdr_maxquant_msms"
      ]
    },
    {
      "page": "read_dfdr_mzid",
      "title": "Read mzIdentML into a 'dfdr_tbl' (generic; score-based TDC q-values)",
      "topics": [
        "read_dfdr_mzid"
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    {
      "page": "read_diann_parquet",
      "title": "Read a DIA-NN 'report.parquet'",
      "topics": [
        "read_diann_parquet"
      ]
    },
    {
      "page": "read_mokapot_psms",
      "title": "Read mokapot PSM text outputs (targets + decoys) and combine",
      "topics": [
        "read_mokapot_psms"
      ]
    },
    {
      "page": "read_spectronaut",
      "title": "Read a Spectronaut TSV report",
      "topics": [
        "read_spectronaut"
      ]
    },
    {
      "page": "read_spectronaut_efficient",
      "title": "Read Spectronaut efficiently with column selection",
      "topics": [
        "read_spectronaut_efficient"
      ]
    },
    {
      "page": "score_to_pvalue",
      "title": "Convert identification scores to p-values or pseudo-p-values",
      "topics": [
        "score_to_pvalue"
      ]
    },
    {
      "page": "spectronaut_runxprecursor",
      "title": "Spectronaut -> run-by-precursor universe (deduplicated within run by 'EG.PrecursorId')",
      "topics": [
        "spectronaut_runxprecursor"
      ]
    }
  ],
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  "_vignettes": [
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      "filename": "diann.html",
      "title": "diagFDR: DIA-NN diagnostics from report.parquet",
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      "headings": [
        "Recommended DIA-NN export settings",
        "Runnable toy example (no DIA-NN files required)",
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      "headings": [
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        "Tail support and stability versus threshold",
        "Local boundary support and elasticity",
        "Equal-chance plausibility by q-band",
        "Real mzIdentML workflow (.mzid)",
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      ],
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      "title": "diagFDR: MaxQuant diagnostics from msms.txt",
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        "Runnable toy example (no external files required)",
        "Headline stability at 1%",
        "Decoy tail support and stability proxy",
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        "Real MaxQuant workflow (msms.txt)",
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      "title": "diagFDR: mokapot diagnostics (competed winners)",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Runnable toy example (no external files required)",
        "Headline stability at 1%",
        "Decoy tail support and stability proxy",
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        "Equal-chance plausibility by q-band (internal check)",
        "PEP reliability and expected errors (ΣPEP)",
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