New package: r-missmethyl (#23140)

1 files changed, 48 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/r-missmethyl/package.py b/var/spack/repos/builtin/packages/r-missmethyl/package.py
new file mode 100644
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+++ b/var/spack/repos/builtin/packages/r-missmethyl/package.py
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+# Copyright 2013-2021 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 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('1.24.0', 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'))