{
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  "Package": "dmsa",
  "Title": "Directional Methylation Set Analysis",
  "Version": "0.99.20",
  "Authors@R": "c(person(\"Tsachi\", \"Ein-Dor\", role = c(\"aut\", \"cre\", \"fnd\"),\nemail = \"teindor@runi.ac.il\",\ncomment = c(ORCID = \"0000-0002-3078-7591\")))",
  "URL": "https://github.com/teindor/dmsa, https://teindor.github.io/dmsa",
  "BugReports": "https://github.com/teindor/dmsa/issues",
  "Description": "Aligns probe-level methylation effects to their predicted\neffect on gene expression and, for system-level analysis, to\neach gene's curated polarity with respect to the system's\nactivation tone (e.g. NR3C1 opposes HPA-axis activation). Pools\nthe aligned coefficients with fixed-sign or expected-sign\nestimators and reports coverage and activation/brake balance\nper set. Ships the Project Alpha gene-system map, a\ngene-to-system polarity table carrying a stated source and\nreview flag on every row, and a curated system > module > gene\n> probe selection cascade whose module labels carry\nliterature-audited evidence tiers and citations; genes without\na polarity entry must be specified by the user.",
  "License": "MIT + file LICENSE",
  "Encoding": "UTF-8",
  "biocViews": "DNAMethylation, DifferentialMethylation, MethylationArray,\nGeneSetEnrichment, GeneExpression, Epigenetics, Microarray,\nCoverage, StatisticalMethod, MultipleComparison, Regression,\nSoftware",
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  "Repository": "https://biocstaging.r-universe.dev",
  "Date/Publication": "2026-10-16 11:48:37 UTC",
  "RemoteUrl": "https://github.com/BiocStaging/dmsa",
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  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-10-17 09:36:29 UTC",
    "User": "root"
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  "Author": "Tsachi Ein-Dor [aut, cre, fnd] (ORCID:\n<https://orcid.org/0000-0002-3078-7591>)",
  "Maintainer": "Tsachi Ein-Dor <teindor@runi.ac.il>",
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  "_created": "2026-10-17T09:36:29.000Z",
  "_published": "2026-10-17T09:50:13.373Z",
  "_buildurl": "https://github.com/r-universe/biocstaging/actions/runs/39021505407",
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    "author": "Tsachi Ein Dor <teindor@idc.ac.il>",
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    "message": "dmsa 0.99.20: every usage argument documented (Rd usage WARNING cleared; duplicated progress/beep removed from dmsa_report.Rd); figure-displays test helper reads PDFs as latin1 bytes (no locale warnings on macOS); NEWS. No engine change.\n",
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    "alpha_gene_systems",
    "alpha_polarity",
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    "dmsa_relweights",
    "dmsa_report",
    "dmsa_report_panels",
    "dmsa_save_analysis_set",
    "dmsa_score",
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    "dmsa_se",
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    "dmsa_sets",
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    "dmsa_test_drive",
    "dmsa_transmit",
    "dmsa_tree",
    "dmsa_triangulate",
    "dmsa_write_coords"
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      "title": "Project Alpha build contracts",
      "topics": [
        "alpha_design"
      ]
    },
    {
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      "title": "Alpha panel gene -> system map (bundled)",
      "topics": [
        "alpha_gene_systems"
      ]
    },
    {
      "page": "alpha_polarity",
      "title": "Alpha panel gene -> system-activation polarity (bundled)",
      "topics": [
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      ]
    },
    {
      "page": "alpha_reference",
      "title": "The bundled Project Alpha biological reference",
      "topics": [
        "alpha_reference"
      ]
    },
    {
      "page": "alpha_reference_check",
      "title": "Integrity of the bundled Alpha biological reference",
      "topics": [
        "alpha_reference_check"
      ]
    },
    {
      "page": "dmsa_align",
      "title": "Build the aligned sign s_j for a set of probes",
      "topics": [
        "dmsa_align"
      ]
    },
    {
      "page": "dmsa_balance",
      "title": "Per-system coverage and polarity balance",
      "topics": [
        "dmsa_balance"
      ]
    },
    {
      "page": "dmsa_bfdr_select",
      "title": "Select units by Bayesian FDR",
      "topics": [
        "dmsa_bfdr_select"
      ]
    },
    {
      "page": "dmsa_cascade",
      "title": "Gated hierarchical DMSA with level-specific inference",
      "topics": [
        "dmsa_cascade"
      ]
    },
    {
      "page": "dmsa_cascade_null",
      "title": "Null statistics for cascade calibration",
      "topics": [
        "dmsa_cascade_null"
      ]
    },
    {
      "page": "dmsa_change",
      "title": "Two-wave change-score DMSA on a common longitudinal scale",
      "topics": [
        "dmsa_change"
      ]
    },
    {
      "page": "dmsa_check_design",
      "title": "Validate a design against the data before fitting",
      "topics": [
        "dmsa_check_design"
      ]
    },
    {
      "page": "dmsa_concordance",
      "title": "Dyadic concordance at every level of the hierarchy, and what it predicts",
      "topics": [
        "dmsa_concordance"
      ]
    },
    {
      "page": "dmsa_contract",
      "title": "Declare one frame's analysis contract",
      "topics": [
        "dmsa_contract"
      ]
    },
    {
      "page": "dmsa_contrast_adjust",
      "title": "Correct p-values across the contrasts of one categorical exposure",
      "topics": [
        "dmsa_contrast_adjust"
      ]
    },
    {
      "page": "dmsa_contrasts",
      "title": "Expand a categorical focal exposure into one directional design per contrast",
      "topics": [
        "dmsa_contrasts"
      ]
    },
    {
      "page": "dmsa_coverage",
      "title": "Coverage report: the reference vs the testable data",
      "topics": [
        "dmsa_coverage"
      ]
    },
    {
      "page": "dmsa_cpg_columns",
      "title": "Select CpG measurement columns by name pattern",
      "topics": [
        "dmsa_cpg_columns"
      ]
    },
    {
      "page": "dmsa_design",
      "title": "Declare a DMSA design: covariates, dependence, and permutation blocks",
      "topics": [
        "dmsa_design"
      ]
    },
    {
      "page": "dmsa_directions",
      "title": "The direction calls DMSA ships with",
      "topics": [
        "dmsa_directions"
      ]
    },
    {
      "page": "dmsa_evidence",
      "title": "Module-level evidence and citations for a cascade, selection or frame",
      "topics": [
        "dmsa_evidence"
      ]
    },
    {
      "page": "dmsa_fit",
      "title": "Fit, pool and permute a DMSA set test under a declared design",
      "topics": [
        "dmsa_fit"
      ]
    },
    {
      "page": "dmsa_frame",
      "title": "Declare a DMSA analysis frame",
      "topics": [
        "dmsa_frame"
      ]
    },
    {
      "page": "dmsa_gate",
      "title": "Gated hierarchical DMSA: one score, one model, level-local correction",
      "topics": [
        "dmsa_gate"
      ]
    },
    {
      "page": "dmsa_gene_model",
      "title": "A gene's exon, intron and UTR structure on real coordinates",
      "topics": [
        "dmsa_gene_model"
      ]
    },
    {
      "page": "dmsa_gene_model_check",
      "title": "Check a gene model before drawing from it",
      "topics": [
        "dmsa_gene_model_check"
      ]
    },
    {
      "page": "dmsa_import",
      "title": "Import a preprocessing pipeline's result for DMSA",
      "topics": [
        "dmsa_import",
        "dmsa_import.character",
        "dmsa_import.data.frame",
        "dmsa_import.default",
        "dmsa_import.list",
        "dmsa_import.matrix"
      ]
    },
    {
      "page": "dmsa_levels",
      "title": "Gated hierarchical DMSA on the pooled aligned statistic",
      "topics": [
        "dmsa_levels"
      ]
    },
    {
      "page": "dmsa_lfdr",
      "title": "Local false discovery rate by central matching",
      "topics": [
        "dmsa_lfdr"
      ]
    },
    {
      "page": "dmsa_mediate",
      "title": "Latent moderated mediation over DMSA system tones",
      "topics": [
        "dmsa_mediate"
      ]
    },
    {
      "page": "dmsa_model",
      "title": "One model, block-permutation calibrated, for any term",
      "topics": [
        "dmsa_model"
      ]
    },
    {
      "page": "dmsa_model_omnibus",
      "title": "Omnibus across the score projections",
      "topics": [
        "dmsa_model_omnibus"
      ]
    },
    {
      "page": "dmsa_moderate",
      "title": "Moderated DMSA (mDMSA)",
      "topics": [
        "dmsa_moderate"
      ]
    },
    {
      "page": "dmsa_modmed",
      "title": "General moderated mediation over observed and latent roles",
      "topics": [
        "dmsa_modmed"
      ]
    },
    {
      "page": "dmsa_mvalues",
      "title": "M-value transform with clamping",
      "topics": [
        "dmsa_mvalues"
      ]
    },
    {
      "page": "dmsa_n_modmed",
      "title": "Sample size for a target power of the moderated-mediation index (or any estimand)",
      "topics": [
        "dmsa_n_modmed"
      ]
    },
    {
      "page": "dmsa_omnibus",
      "title": "Directionless omnibus test of a categorical focal exposure over a set",
      "topics": [
        "dmsa_omnibus"
      ]
    },
    {
      "page": "dmsa_outcome",
      "title": "Test an aligned tone score against a non-Gaussian outcome",
      "topics": [
        "dmsa_outcome"
      ]
    },
    {
      "page": "dmsa_pdance",
      "title": "The p-dance test: does a finding's p-value survive a change of analysis set?",
      "topics": [
        "dmsa_pdance"
      ]
    },
    {
      "page": "dmsa_perm_pvalue",
      "title": "Permutation p-value for a DMSA statistic",
      "topics": [
        "dmsa_perm_pvalue"
      ]
    },
    {
      "page": "dmsa_plot_genes",
      "title": "Panel 2: gene level inside one system",
      "topics": [
        "dmsa_plot_genes"
      ]
    },
    {
      "page": "dmsa_plot_locus",
      "title": "Locus figure: chromosome, gene with CpG lollipops, and per-CpG effects",
      "topics": [
        "dmsa_plot_locus"
      ]
    },
    {
      "page": "dmsa_plot_locus_gviz",
      "title": "The locus panel drawn by Gviz",
      "topics": [
        "dmsa_plot_locus_gviz"
      ]
    },
    {
      "page": "dmsa_plot_probes",
      "title": "Panel 3: probe level, with the CpG-to-expression direction applied",
      "topics": [
        "dmsa_plot_probes"
      ]
    },
    {
      "page": "dmsa_plot_systems",
      "title": "Panel 1: dense arm against sparse arm, every system",
      "topics": [
        "dmsa_plot_systems"
      ]
    },
    {
      "page": "dmsa_polarity",
      "title": "Load a gene-to-system polarity table",
      "topics": [
        "dmsa_polarity"
      ]
    },
    {
      "page": "dmsa_polarity_check",
      "title": "Validate a candidate polarity table",
      "topics": [
        "dmsa_polarity_check"
      ]
    },
    {
      "page": "dmsa_polarity_fetch",
      "title": "Draft polarity signs for a panel from public databases",
      "topics": [
        "dmsa_polarity_fetch"
      ]
    },
    {
      "page": "dmsa_polarity_for",
      "title": "Polarity table for one system, in the form dmsa_align() wants",
      "topics": [
        "dmsa_polarity_for"
      ]
    },
    {
      "page": "dmsa_polarity_review",
      "title": "Rows of a polarity table that need a human decision",
      "topics": [
        "dmsa_polarity_review"
      ]
    },
    {
      "page": "dmsa_polarity_sources",
      "title": "Which public resources DMSA can draft polarity from, and what each is good for",
      "topics": [
        "dmsa_polarity_sources"
      ]
    },
    {
      "page": "dmsa_power_concordance",
      "title": "Power for dyadic concordance at one level, its outcome surface and its exposure form",
      "topics": [
        "dmsa_power_concordance",
        "dmsa_power_exposure",
        "dmsa_power_surface"
      ]
    },
    {
      "page": "dmsa_power_modmed",
      "title": "Power for moderated mediation (and plain mediation) through the package estimator",
      "topics": [
        "dmsa_power_modmed"
      ]
    },
    {
      "page": "dmsa_power_slope",
      "title": "Power and sample size for a single (partial) slope between error-prone scores",
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      "page": "dmsa_power_transmit",
      "title": "Power for the parent-to-child paired slope at one level of the hierarchy",
      "topics": [
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      "page": "dmsa_probe_annotation_template",
      "title": "Write a template script that fetches probe coordinates from Bioconductor",
      "topics": [
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      "page": "dmsa_probe_coords",
      "title": "Probe genomic coordinates, without Bioconductor",
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      "title": "Construct a DMSA reference bundle",
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      "page": "dmsa_reference_csv",
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      "title": "Subject-level aligned tone score",
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