Package: crossarrayEWAS
Type: Package
Title: Design-Aware Region and Block Detection for Cross-Array
        Longitudinal EWAS
Version: 0.99.1
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: GenomicRanges, IRanges, Matrix, S4Vectors,
        SummarizedExperiment, jsonlite, limma, methods, stats
Suggests: testthat (>= 3.0.0), knitr, rmarkdown, BiocStyle, minfi,
        IlluminaHumanMethylation450kanno.ilmn12.hg19,
        IlluminaHumanMethylationEPICanno.ilm10b4.hg19
VignetteBuilder: knitr
biocViews: DNAMethylation, DifferentialMethylation, Epigenetics,
        MethylationArray, Regression, Software
BiocType: Software
URL: https://github.com/bioinfbrad/crossarrayEWAS
BugReports: https://github.com/bioinfbrad/crossarrayEWAS/issues
Config/testthat/edition: 3
Roxygen: list(markdown = TRUE)
Config/roxygen2/version: 8.1.0
git_url: https://git.bioconductor.org/packages/crossarrayEWAS
git_branch: devel
git_last_commit: c865b48
git_last_commit_date: 2026-10-12
Repository: Bioconductor 3.24
Date/Publication: 2026-11-08
NeedsCompilation: no
Packaged: 2026-11-08 22:24:04 UTC; biocbuild
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>
