r-qvalue: Create new package. (#6137)

1 files changed, 50 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/r-qvalue/package.py b/var/spack/repos/builtin/packages/r-qvalue/package.py
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+##############################################################################
+# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/spack/spack
+# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RQvalue(RPackage):
+    """This package takes a list of p-values resulting from the
+    simultaneous testing of many hypotheses and estimates their
+    q-values and local FDR values. The q-value of a test measures
+    the proportion of false positives incurred (called the false
+    discovery rate) when that particular test is called significant.
+    The local FDR measures the posterior probability the null
+    hypothesis is true given the test's p-value. Various plots are
+    automatically generated, allowing one to make sensible
+    significance cut-offs. Several mathematical results have
+    recently been shown on the conservative accuracy of the
+    estimated q-values from this software. The software can be
+    applied to problems in genomics, brain imaging, astrophysics,
+    and data mining."""
+
+    homepage = "https://www.bioconductor.org/packages/qvalue/"
+    url      = "https://git.bioconductor.org/packages/qvalue"
+
+    version('2.8.0', git='https://git.bioconductor.org/packages/qvalue', commit='c7bf3315619d42d800f57a36670c25a7495ded72')
+
+    depends_on('r@3.4.0:3.4.9', when='@2.8.0')
+    depends_on('r-ggplot2', type=('build', 'run'))
+    depends_on('r-reshape2', type=('build', 'run'))