# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)

from spack.package import *


class RMissmethyl(RPackage):
    """Analysing Illumina HumanMethylation BeadChip Data.

    Normalisation, testing for differential variability and differential
    methylation and gene set testing for data from Illumina's Infinium
    HumanMethylation arrays. The normalisation procedure is subset-quantile
    within-array normalisation (SWAN), which allows Infinium I and II type
    probes on a single array to be normalised together. The test for
    differential variability is based on an empirical Bayes version of Levene's
    test. Differential methylation testing is performed using RUV, which can
    adjust for systematic errors of unknown origin in high-dimensional data by
    using negative control probes. Gene ontology analysis is performed by
    taking into account the number of probes per gene on the array, as well as
    taking into account multi-gene associated probes."""

    bioc = "missMethyl"

    version("1.34.0", commit="57db57c48ab79c36eb89726afc2833a981cbaf3d")
    version("1.32.0", commit="969b892e400b9821398099bcea46f2d0431daedf")
    version("1.30.0", commit="734846653f332f10e557b87aca4cb5d100b62469")
    version("1.28.0", commit="6a36aee28837736291ac630c1da3909f0e9c8d6a")
    version("1.24.0", commit="f6c86048911dc0e302fb593b7d0623f6e77ac332")

    depends_on("r@3.6.0:", type=("build", "run"))
    depends_on("r-illuminahumanmethylation450kanno-ilmn12-hg19", type=("build", "run"))
    depends_on("r-illuminahumanmethylationepicanno-ilm10b4-hg19", type=("build", "run"))
    depends_on("r-annotationdbi", type=("build", "run"))
    depends_on("r-biasedurn", type=("build", "run"))
    depends_on("r-biobase", type=("build", "run"))
    depends_on("r-biocgenerics", type=("build", "run"))
    depends_on("r-genomicranges", type=("build", "run"))
    depends_on("r-go-db", type=("build", "run"))
    depends_on("r-illuminahumanmethylation450kmanifest", type=("build", "run"))
    depends_on("r-illuminahumanmethylationepicmanifest", type=("build", "run"))
    depends_on("r-iranges", type=("build", "run"))
    depends_on("r-limma", type=("build", "run"))
    depends_on("r-methylumi", type=("build", "run"))
    depends_on("r-minfi", type=("build", "run"))
    depends_on("r-org-hs-eg-db", type=("build", "run"))
    depends_on("r-ruv", type=("build", "run"))
    depends_on("r-s4vectors", type=("build", "run"))
    depends_on("r-statmod", type=("build", "run"))
    depends_on("r-stringr", type=("build", "run"))
    depends_on("r-summarizedexperiment", type=("build", "run"))