Package: tewas
Type: Package
Title: Unit-Level Multiple Testing for Epigenome-Wide Association
        Studies 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",
                  role = c("aut", "cre"), comment = c(ORCID = "0000-0002-3078-7591"))
Description: A multiple-testing engine for DNA methylation arrays
        (engine v1.6) and a frame layer for the designs of behavioral
        epigenetics. Probes are grouped into genomic-run units; each
        unit is tested with four complementary statistics (dense sum,
        coherence-gated flip, Simes, kernel matched filter) whose null
        distributions come from one shared permutation stream with a
        calibrated exponential tail below the permutation floor; the
        arm p-values are combined by the Cauchy combination and units
        are selected by weighted Benjamini-Hochberg with cross-fitted
        structural weights and, optionally, a per-probe knowledge prior
        from longitudinal within-person change measured in an external
        cohort. Anchor probes carried in the scan measure whether the
        prior is licensed (the lens) and whether the scan's null is
        calibrated (the inflation guard, read on an alive null ruler);
        the prior is tempered toward zero when it is not, and nothing
        is corrected. The frame layer declares a design (moderation,
        curvature, threshold, acceleration, methylation as predictor or
        as outcome), runs every arm through the same engine, merges
        selected units into regions with coordinates, annotates the
        probes with their target genes, and writes tables, trajectory
        figures and a self-declaring summary. Unit-level FDR is
        controlled under the stated assumptions; probe-level false
        discovery and the calibration of every arm were measured in
        registered simulations whose readings the package prints beside
        its results. The anchor panel and the alive ruler are shipped
        under inst/extdata as per-probe summaries only. Input is a beta
        matrix or a SummarizedExperiment (a minfi GenomicRatioSet
        included); selected regions, units and probes are returned as
        GRanges on request.
License: MIT + file LICENSE
Encoding: UTF-8
Depends: R (>= 4.5.0)
Imports: stats, utils, graphics, grDevices, methods, data.table,
        GenomicRanges, IRanges, SummarizedExperiment
Suggests: viridisLite, cpgdirection, knitr, rmarkdown, BiocStyle
VignetteBuilder: knitr
biocViews: DNAMethylation, MethylationArray, Epigenetics,
        MultipleComparison, StatisticalMethod, DifferentialMethylation,
        GeneRegulation, Software
URL: https://github.com/teindor/tewas
BugReports: https://github.com/teindor/tewas/issues
RoxygenNote: 7.3.2
Config/pak/sysreqs: zlib1g-dev
Repository: https://biocstaging.r-universe.dev
Date/Publication: 2026-09-15 11:59:02 UTC
RemoteUrl: https://github.com/BiocStaging/tewas
RemoteRef: HEAD
RemoteSha: a806dea26df498f4db1036cd8c4034d19352bdf3
NeedsCompilation: no
Packaged: 2026-10-15 11:04:41 UTC; root
Author: Tsachi Ein-Dor [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-3078-7591>)
Maintainer: Tsachi Ein-Dor <teindor@runi.ac.il>