{
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  "Title": "Unit-Level Multiple Testing for Epigenome-Wide Association\nStudies with an Anchor-Calibrated Knowledge Prior",
  "Version": "0.99.2",
  "Date": "2026-09-15",
  "Authors@R": "person(\"Tsachi\", \"Ein-Dor\", email = \"teindor@runi.ac.il\",\nrole = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-3078-7591\"))",
  "Description": "A multiple-testing engine for DNA methylation arrays\n(engine v1.6) and a frame layer for the designs of behavioral\nepigenetics. Probes are grouped into genomic-run units; each\nunit is tested with four complementary statistics (dense sum,\ncoherence-gated flip, Simes, kernel matched filter) whose null\ndistributions come from one shared permutation stream with a\ncalibrated exponential tail below the permutation floor; the\narm p-values are combined by the Cauchy combination and units\nare selected by weighted Benjamini-Hochberg with cross-fitted\nstructural weights and, optionally, a per-probe knowledge prior\nfrom longitudinal within-person change measured in an external\ncohort. Anchor probes carried in the scan measure whether the\nprior is licensed (the lens) and whether the scan's null is\ncalibrated (the inflation guard, read on an alive null ruler);\nthe prior is tempered toward zero when it is not, and nothing\nis corrected. The frame layer declares a design (moderation,\ncurvature, threshold, acceleration, methylation as predictor or\nas outcome), runs every arm through the same engine, merges\nselected units into regions with coordinates, annotates the\nprobes with their target genes, and writes tables, trajectory\nfigures and a self-declaring summary. Unit-level FDR is\ncontrolled under the stated assumptions; probe-level false\ndiscovery and the calibration of every arm were measured in\nregistered simulations whose readings the package prints beside\nits results. The anchor panel and the alive ruler are shipped\nunder inst/extdata as per-probe summaries only. Input is a beta\nmatrix or a SummarizedExperiment (a minfi GenomicRatioSet\nincluded); selected regions, units and probes are returned as\nGRanges on request.",
  "License": "MIT + file LICENSE",
  "Encoding": "UTF-8",
  "VignetteBuilder": "knitr",
  "biocViews": "DNAMethylation, MethylationArray, Epigenetics,\nMultipleComparison, StatisticalMethod, DifferentialMethylation,\nGeneRegulation, Software",
  "URL": "https://github.com/teindor/tewas",
  "BugReports": "https://github.com/teindor/tewas/issues",
  "RoxygenNote": "7.3.2",
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  "Date/Publication": "2026-09-15 11:59:02 UTC",
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  "Author": "Tsachi Ein-Dor [aut, cre] (ORCID:\n<https://orcid.org/0000-0002-3078-7591>)",
  "Maintainer": "Tsachi Ein-Dor <teindor@runi.ac.il>",
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  "_published": "2026-09-15T13:57:52.371Z",
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    "author": "Tsachi Ein Dor <teindor@idc.ac.il>",
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    "statisticalmethod",
    "differentialmethylation",
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    "tewas_simulate",
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      "title": "Anchor table for the engine from the R11 panel (v1.6 roles)",
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      ]
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    {
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      "title": "The tewas engine (v1.6): units, four arms, one permutation stream, weighted BH with the lens-tempered knowledge prior and the inflation guard",
      "topics": [
        "tewas_engine2"
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      "title": "Flip-arm amplitudes by evidence tier",
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        "tewas_flip_J"
      ]
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      "title": "Per-probe statistics of a focal regressor after a nuisance design",
      "topics": [
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      ]
    },
    {
      "page": "tewas_frame",
      "title": "Declare and run a tewas design: DMR-level answers with the probes within",
      "topics": [
        "print.tewas_frame",
        "tewas_frame"
      ]
    },
    {
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      "title": "Annotate the probes, units and DMRs of a tewas_frame with their target genes",
      "topics": [
        "tewas_genes"
      ]
    },
    {
      "page": "tewas_granges",
      "title": "Selected regions, units or probes of a tewas result as a GRanges",
      "topics": [
        "tewas_granges"
      ]
    },
    {
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      "title": "Rank-inverse-normal transform (the v1.7 rule for continuous outcomes)",
      "topics": [
        "tewas_inverse_normal"
      ]
    },
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      "title": "Load a shipped anchor panel",
      "topics": [
        "tewas_panel"
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    },
    {
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      "title": "Removability diagnostic (the v1.7 rule, report-only)",
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      "topics": [
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      ]
    },
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      "topics": [
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    },
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