Package: crossarrayEWAS
Type: Package
Title: Design-Aware Region and Block Detection for Cross-Array
        Longitudinal EWAS
Version: 0.99.0
Authors@R: c(
    person("Katarzyna", "Kamieniecka", role = c("aut", "cre"),
           email = "kkamieni@bradford.ac.uk",
           comment = c(ORCID = "0009-0004-2454-5950")),
    person("Samantha", "McLean", role = "aut",
           email = "S.L.Mclean@bradford.ac.uk",
           comment = c(ORCID = "0000-0001-9328-8928")),
    person("Krzysztof", "Poterlowicz", role = "aut",
           email = "K.Poterlowicz1@bradford.ac.uk",
           comment = c(ORCID = "0000-0001-6173-5674")))
Description: Estimation and region-calling routines for epigenome-wide
        association studies that combine Illumina HumanMethylation450
        and MethylationEPIC samples and follow subjects over more than
        one visit. Probe-level effects are fitted within subject, so
        subject identity, array type and chip are absorbed rather than
        modelled; adjacent probes are grouped by within-subject
        co-methylation; regions are obtained by total-variation
        denoising with a distance-decaying penalty, which places
        boundaries where the effect track jumps instead of thresholding
        a smooth curve; and long-range blocks are called from a
        three-state hidden semi-Markov model whose transition
        probabilities decay with genomic distance. Selection stability
        and permutation nulls resample subjects, not samples, so a
        subject's visit series is never split.
License: MIT + file LICENSE
Encoding: UTF-8
Depends: R (>= 4.5.0)
Imports: Matrix, jsonlite, limma, methods, stats
Suggests: testthat (>= 3.0.0), knitr, rmarkdown, BiocStyle,
        SummarizedExperiment, GenomicRanges, S4Vectors, IRanges
VignetteBuilder: knitr
biocViews: DNAMethylation, DifferentialMethylation, Epigenetics,
        MethylationArray, Regression, Software
BiocType: Software
URL: https://github.com/kkamieniecka/ewas-crossarray-harmonise
BugReports: https://github.com/kkamieniecka/ewas-crossarray-harmonise/issues
Config/testthat/edition: 3
Config/roxygen2/version: 8.1.0
Repository: https://biocstaging.r-universe.dev
Date/Publication: 2026-09-16 11:04:59 UTC
RemoteUrl: https://github.com/BiocStaging/crossarrayEWAS
RemoteRef: HEAD
RemoteSha: c2cad196d6af608fb219284c1d23f07e32985721
NeedsCompilation: no
Packaged: 2026-09-17 13:43:31 UTC; root
Author: Katarzyna Kamieniecka [aut, cre] (ORCID:
    <https://orcid.org/0009-0004-2454-5950>),
  Samantha McLean [aut] (ORCID: <https://orcid.org/0000-0001-9328-8928>),
  Krzysztof Poterlowicz [aut] (ORCID:
    <https://orcid.org/0000-0001-6173-5674>)
Maintainer: Katarzyna Kamieniecka <kkamieni@bradford.ac.uk>