Package: SEAGLE
Type: Package
Title: Scalable Exact Algorithm for Large-Scale Set-Based
        Gene-Environment Interaction Tests
Version: 1.0.1
Authors@R: c(person("Jocelyn", "Chi", email = "jocetchi@gmail.com",
                  role = c("aut", "cre")),
            person("Ilse", "Ipsen", email = "ipsen@ncsu.edu",
                  role = c("aut")),
            person("Jung-Ying", "Tzeng", email = "jytzeng@ncsu.edu",
                  role = c("aut"))
                  )
Description: The explosion of biobank data offers immediate
        opportunities for gene-environment (GxE) interaction studies of
        complex diseases because of the large sample sizes and rich
        collection in genetic and non-genetic information. However, the
        extremely large sample size also introduces new computational
        challenges in GxE assessment, especially for set-based GxE
        variance component (VC) tests, a widely used strategy to boost
        overall GxE signals and to evaluate the joint GxE effect of
        multiple variants from a biologically meaningful unit (e.g.,
        gene). We present 'SEAGLE', a Scalable Exact AlGorithm for
        Large-scale Set-based GxE tests, to permit GxE VC test scalable
        to biobank data. 'SEAGLE' employs modern matrix computations to
        achieve the same “exact” results as the original GxE VC tests,
        and does not impose additional assumptions nor relies on
        approximations. 'SEAGLE' can easily accommodate sample sizes in
        the order of 10^5, is implementable on standard laptops, and
        does not require specialized equipment. The accompanying
        manuscript for this package can be found at Chi, Ipsen, Hsiao,
        Lin, Wang, Lee, Lu, and Tzeng. (2021+) <arXiv:2105.03228>.
URL: https://github.com/jocelynchi/SEAGLE
License: GPL-3
Depends: R (>= 3.5.0), Matrix, CompQuadForm
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
Suggests: rmarkdown, knitr
VignetteBuilder: knitr
Repository: https://jocelynchi.r-universe.dev
Date/Publication: 2021-11-05 21:29:54 UTC
RemoteUrl: https://github.com/jocelynchi/seagle
RemoteRef: HEAD
RemoteSha: ee5d2a5d15cce39c295fa30532771556ec85230e
NeedsCompilation: no
Packaged: 2026-06-12 09:53:19 UTC; root
Author: Jocelyn Chi [aut, cre],
  Ilse Ipsen [aut],
  Jung-Ying Tzeng [aut]
Maintainer: Jocelyn Chi <jocetchi@gmail.com>