File R-asmbPLS.spec of Package R-asmbPLS
# Automatically generated by CRAN2OBS
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# Spec file for package asmbPLS
# This file is auto-generated using information in the package source,
# esp. Description and Summary. Improvements in that area should be
# discussed with upstream.
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%global packname asmbPLS
%global rlibdir %{_libdir}/R/library
Name: R-%{packname}
Version: 1.0.0
Release: 0
Summary: Predicting and Classifying Patient Phenotypes with Multi-Omics Data
Group: Development/Libraries/Other
License: GPL (>= 2)
URL: http://cran.r-project.org/web/packages/%{packname}
Source: asmbPLS_1.0.0.tar.gz
Requires: R-base
Requires: R-Rcpp
Requires: R-ggplot2
Requires: R-ggpubr
Requires: R-RcppArmadillo
Requires: R-cli
Requires: R-gtable
Requires: R-isoband
Requires: R-lifecycle
Requires: R-rlang
Requires: R-S7
Requires: R-scales
Requires: R-vctrs
Requires: R-withr
Requires: R-ggrepel
Requires: R-ggsci
Requires: R-tidyr
Requires: R-purrr
Requires: R-dplyr
Requires: R-cowplot
Requires: R-ggsignif
Requires: R-gridExtra
Requires: R-glue
Requires: R-polynom
Requires: R-rstatix
Requires: R-tibble
Requires: R-magrittr
Requires: R-generics
Requires: R-pillar
Requires: R-R6
Requires: R-tidyselect
Requires: R-broom
Requires: R-corrplot
Requires: R-car
Requires: R-farver
Requires: R-labeling
Requires: R-RColorBrewer
Requires: R-viridisLite
Requires: R-pkgconfig
Requires: R-stringr
Requires: R-cpp11
Requires: R-backports
Requires: R-carData
Requires: R-abind
Requires: R-Formula
Requires: R-pbkrtest
Requires: R-quantreg
Requires: R-lme4
Requires: R-utf8
Requires: R-stringi
Requires: R-minqa
Requires: R-nloptr
Requires: R-reformulas
Requires: R-RcppEigen
Requires: R-numDeriv
Requires: R-doBy
Requires: R-SparseM
Requires: R-MatrixModels
Requires: R-Deriv
Requires: R-modelr
Requires: R-microbenchmark
Requires: R-Rdpack
Requires: R-rbibutils
# %%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-Rcpp-devel
BuildRequires: R-ggplot2
BuildRequires: R-ggpubr
BuildRequires: R-RcppArmadillo-devel
BuildRequires: R-cli
BuildRequires: R-gtable
BuildRequires: R-isoband
BuildRequires: R-lifecycle
BuildRequires: R-rlang
BuildRequires: R-S7
BuildRequires: R-scales
BuildRequires: R-vctrs
BuildRequires: R-withr
BuildRequires: R-ggrepel
BuildRequires: R-ggsci
BuildRequires: R-tidyr
BuildRequires: R-purrr
BuildRequires: R-dplyr
BuildRequires: R-cowplot
BuildRequires: R-ggsignif
BuildRequires: R-gridExtra
BuildRequires: R-glue
BuildRequires: R-polynom
BuildRequires: R-rstatix
BuildRequires: R-tibble
BuildRequires: R-magrittr
BuildRequires: R-generics
BuildRequires: R-pillar
BuildRequires: R-R6
BuildRequires: R-tidyselect
BuildRequires: R-broom
BuildRequires: R-corrplot
BuildRequires: R-car
BuildRequires: R-farver
BuildRequires: R-labeling
BuildRequires: R-RColorBrewer
BuildRequires: R-viridisLite
BuildRequires: R-pkgconfig
BuildRequires: R-stringr
BuildRequires: R-cpp11-devel
BuildRequires: R-backports
BuildRequires: R-carData
BuildRequires: R-abind
BuildRequires: R-Formula
BuildRequires: R-pbkrtest
BuildRequires: R-quantreg
BuildRequires: R-lme4
BuildRequires: R-utf8
BuildRequires: R-stringi
BuildRequires: R-minqa
BuildRequires: R-nloptr
BuildRequires: R-reformulas
BuildRequires: R-RcppEigen-devel
BuildRequires: R-numDeriv
BuildRequires: R-doBy
BuildRequires: R-SparseM
BuildRequires: R-MatrixModels
BuildRequires: R-Deriv
BuildRequires: R-modelr
BuildRequires: R-microbenchmark
BuildRequires: R-Rdpack
BuildRequires: R-rbibutils
BuildRequires: gcc gcc-c++ gcc-fortran
Suggests: R-knitr
Suggests: R-rmarkdown
%description
Adaptive Sparse Multi-block Partial Least Square, a supervised
algorithm, is an extension of the Sparse Multi-block Partial Least
Square, which allows different quantiles to be used in different blocks
of different partial least square components to decide the proportion
of features to be retained. The best combinations of quantiles can be
chosen from a set of user-defined quantiles combinations by
cross-validation. By doing this, it enables us to do the feature
selection for different blocks, and the selected features can then be
further used to predict the outcome. For example, in biomedical
applications, clinical covariates plus different types of omics data
such as microbiome, metabolome, mRNA data, methylation data, copy
number variation data might be predictive for patients outcome such as
survival time or response to therapy. Different types of data could be
put in different blocks and along with survival time to fit the model.
The fitted model can then be used to predict the survival for the new
samples with the corresponding clinical covariates and omics data. In
addition, Adaptive Sparse Multi-block Partial Least Square Discriminant
Analysis is also included, which extends Adaptive Sparse Multi-block
Partial Least Square for classifying the categorical outcome.
%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}
%{rlibdir}/%{packname}/CITATION
%doc %{rlibdir}/%{packname}/DESCRIPTION
%{rlibdir}/%{packname}/INDEX
%{rlibdir}/%{packname}/Meta
%{rlibdir}/%{packname}/NAMESPACE
%{rlibdir}/%{packname}/R
%{rlibdir}/%{packname}/data
%{rlibdir}/%{packname}/doc
%doc %{rlibdir}/%{packname}/help
%doc %{rlibdir}/%{packname}/html
%{rlibdir}/%{packname}/libs
%changelog
