File R-mvMAPIT.spec of Package R-mvMAPIT
# Automatically generated by CRAN2OBS
#
# Spec file for package mvMAPIT
# This file is auto-generated using information in the package source,
# esp. Description and Summary. Improvements in that area should be
# discussed with upstream.
#
# Copyright (c) 2025 SUSE LINUX GmbH, Nuernberg, Germany.
#
# All modifications and additions to the file contributed by third parties
# remain the property of their copyright owners, unless otherwise agreed
# upon. The license for this file, and modifications and additions to the
# file, is the same license as for the pristine package itself (unless the
# license for the pristine package is not an Open Source License, in which
# case the license is the MIT License). An "Open Source License" is a
# license that conforms to the Open Source Definition (Version 1.9)
# published by the Open Source Initiative.
#
# Please submit bugfixes or comments via http://bugs.opensuse.org/
#
%global packname mvMAPIT
%global rlibdir %{_libdir}/R/library
Name: R-%{packname}
Version: 2.0.3
Release: 0
Summary: Multivariate Genome Wide Marginal Epistasis Test
Group: Development/Libraries/Other
License: GPL (>= 3)
URL: http://cran.r-project.org/web/packages/%{packname}
Source: mvMAPIT_2.0.3.tar.gz
Requires: R-base
Requires: R-checkmate
Requires: R-CompQuadForm
Requires: R-dplyr
Requires: R-foreach
Requires: R-harmonicmeanp
Requires: R-logging
Requires: R-mvtnorm
Requires: R-Rcpp
Requires: R-tidyr
Requires: R-RcppArmadillo
Requires: R-RcppParallel
Requires: R-RcppProgress
Requires: R-RcppSpdlog
Requires: R-testthat
Requires: R-backports
Requires: R-cli
Requires: R-generics
Requires: R-glue
Requires: R-lifecycle
Requires: R-magrittr
Requires: R-pillar
Requires: R-R6
Requires: R-rlang
Requires: R-tibble
Requires: R-tidyselect
Requires: R-vctrs
Requires: R-iterators
Requires: R-FMStable
Requires: R-brio
Requires: R-callr
Requires: R-desc
Requires: R-digest
Requires: R-evaluate
Requires: R-jsonlite
Requires: R-pkgload
Requires: R-praise
Requires: R-processx
Requires: R-ps
Requires: R-waldo
Requires: R-withr
Requires: R-purrr
Requires: R-stringr
Requires: R-cpp11
Requires: R-utf8
Requires: R-fs
Requires: R-pkgbuild
Requires: R-rprojroot
Requires: R-stringi
Requires: R-pkgconfig
Requires: R-diffobj
Requires: R-crayon
# %%if 0%%{?sle_version} > 120400 || 0%%{?is_opensuse}
# # Three others commonly needed
# BuildRequires: tex(ae.sty)
# BuildRequires: tex(fancyvrb.sty)
# BuildRequires: tex(inconsolata.sty)
# BuildRequires: tex(natbib.sty)
# %else
# BuildRequires: texlive
# %endif
# BuildRequires: texinfo
BuildRequires: fdupes
BuildRequires: R-base
BuildRequires: R-checkmate
BuildRequires: R-CompQuadForm
BuildRequires: R-dplyr
BuildRequires: R-foreach
BuildRequires: R-harmonicmeanp
BuildRequires: R-logging
BuildRequires: R-mvtnorm
BuildRequires: R-Rcpp-devel
BuildRequires: R-tidyr
BuildRequires: R-RcppArmadillo-devel
BuildRequires: R-RcppParallel-devel
BuildRequires: R-RcppProgress
BuildRequires: R-RcppSpdlog-devel
BuildRequires: R-testthat
BuildRequires: R-backports
BuildRequires: R-cli
BuildRequires: R-generics
BuildRequires: R-glue
BuildRequires: R-lifecycle
BuildRequires: R-magrittr
BuildRequires: R-pillar
BuildRequires: R-R6
BuildRequires: R-rlang
BuildRequires: R-tibble
BuildRequires: R-tidyselect
BuildRequires: R-vctrs
BuildRequires: R-iterators
BuildRequires: R-FMStable
BuildRequires: R-brio
BuildRequires: R-callr
BuildRequires: R-desc
BuildRequires: R-digest
BuildRequires: R-evaluate
BuildRequires: R-jsonlite
BuildRequires: R-pkgload
BuildRequires: R-praise
BuildRequires: R-processx
BuildRequires: R-ps
BuildRequires: R-waldo
BuildRequires: R-withr
BuildRequires: R-purrr
BuildRequires: R-stringr
BuildRequires: R-cpp11-devel
BuildRequires: R-utf8
BuildRequires: R-fs
BuildRequires: R-pkgbuild
BuildRequires: R-rprojroot
BuildRequires: R-stringi
BuildRequires: R-pkgconfig
BuildRequires: R-diffobj
BuildRequires: R-crayon
BuildRequires: gcc gcc-c++ gcc-fortran
Suggests: R-GGally
Suggests: R-ggplot2
Suggests: R-ggrepel
Suggests: R-kableExtra
Suggests: R-knitr
Suggests: R-markdown
Suggests: R-RcppAlgos
Suggests: R-rmarkdown
Suggests: R-testthat
%description
Epistasis, commonly defined as the interaction between genetic loci, is
known to play an important role in the phenotypic variation of complex
traits. As a result, many statistical methods have been developed to
identify genetic variants that are involved in epistasis, and nearly
all of these approaches carry out this task by focusing on analyzing
one trait at a time. Previous studies have shown that jointly modeling
multiple phenotypes can often dramatically increase statistical power
for association mapping. In this package, we present the 'multivariate
MArginal ePIstasis Test' ('mvMAPIT') – a multi-outcome generalization
of a recently proposed epistatic detection method which seeks to detect
marginal epistasis or the combined pairwise interaction effects between
a given variant and all other variants. By searching for marginal
epistatic effects, one can identify genetic variants that are involved
in epistasis without the need to identify the exact partners with which
the variants interact – thus, potentially alleviating much of the
statistical and computational burden associated with conventional
explicit search based methods. Our proposed 'mvMAPIT' builds upon this
strategy by taking advantage of correlation structure between traits to
improve the identification of variants involved in epistasis. We
formulate 'mvMAPIT' as a multivariate linear mixed model and develop a
multi-trait variance component estimation algorithm for efficient
parameter inference and P-value computation. Together with reasonable
model approximations, our proposed approach is scalable to moderately
sized genome-wide association studies. Crawford et al. (2017)
<doi:10.1371/journal.pgen.1006869>. Stamp et al. (2023)
<doi:10.1093/g3journal/jkad118>.
%prep
%setup -q -c -n %{packname}
# the next line is needed, because we build without --clean in between two packages
rm -rf ~/.R
%build
%install
mkdir -p %{buildroot}%{rlibdir}
%{_bindir}/R CMD INSTALL -l %{buildroot}%{rlibdir} %{packname}
test -d %{packname}/src && (cd %{packname}/src; rm -f *.o *.so)
rm -f %{buildroot}%{rlibdir}/R.css
%fdupes -s %{buildroot}%{rlibdir}
#%%check
#%%{_bindir}/R CMD check %%{packname}
%files
%dir %{rlibdir}/%{packname}
%doc %{rlibdir}/%{packname}/DESCRIPTION
%{rlibdir}/%{packname}/INDEX
%{rlibdir}/%{packname}/Meta
%{rlibdir}/%{packname}/NAMESPACE
%doc %{rlibdir}/%{packname}/NEWS.md
%{rlibdir}/%{packname}/R
%{rlibdir}/%{packname}/data
%doc %{rlibdir}/%{packname}/doc
%doc %{rlibdir}/%{packname}/help
%doc %{rlibdir}/%{packname}/html
%{rlibdir}/%{packname}/libs
%changelog
