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# Copyright 2013-2019 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 RGofuncr(RPackage):
"""Gene ontology enrichment using FUNC.
GOfuncR performs a gene ontology enrichment analysis based on the
ontology enrichment software FUNC. GO-annotations are obtained from
OrganismDb or OrgDb packages ('Homo.sapiens' by default); the GO-graph
is included in the package and updated regularly (27-Mar-2019). GOfuncR
provides the standard candidate vs. background enrichment analysis using
the hypergeometric test, as well as three additional tests: (i) the
Wilcoxon rank-sum test that is used when genes are ranked, (ii) a
binomial test that is used when genes are associated with two counts and
(iii) a Chi-square or Fisher's exact test that is used in cases when
genes are associated with four counts. To correct for multiple testing
and interdependency of the tests, family-wise error rates are computed
based on random permutations of the gene-associated variables. GOfuncR
also provides tools for exploring the ontology graph and the
annotations, and options to take gene-length or spatial clustering of
genes into account. It is also possible to provide custom gene
coordinates, annotations and ontologies."""
homepage = "https://bioconductor.org/packages/GOfuncR"
git = "https://git.bioconductor.org/packages/GOfuncR.git"
version('1.4.0', commit='2f633dc28e3faeddc5346fcdcadf1c29e3fcf709')
version('1.2.0', commit='140a3cea4fe34d32fef9be756f85e337ce3deded')
version('1.0.0', commit='becd4ddde085c5477042adb856e7a4f40dbd648e')
depends_on('r@3.4:', type=('build', 'run'))
depends_on('r-vioplot@0.2:', type=('build', 'run'))
depends_on('r-rcpp@0.11.5:', type=('build', 'run'))
depends_on('r-mapplots@1.5:', type=('build', 'run'))
depends_on('r-gtools@3.5.0:', type=('build', 'run'))
depends_on('r-genomicranges@1.28.4:', type=('build', 'run'))
depends_on('r-annotationdbi', type=('build', 'run'))
depends_on('r-iranges', when='@1.2.0:', type=('build', 'run'))
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