projects / packages / R-vsn.git / blame
| Commit | Line | Data |
|---|---|---|
| e4e201d4 JR |
1 | %define packname vsn |
| 2 | ||
| 3 | Summary: Variance stabilization and calibration for microarray data | |
| 4 | Name: R-%{packname} | |
| 5 | Version: 3.26.0 | |
| 6 | Release: 1 | |
| 7 | License: Artistic 2.0 | |
| 8 | Group: Applications/Engineering | |
| 9 | Source0: http://bioconductor.org/packages/release/bioc/src/contrib/%{packname}_%{version}.tar.gz | |
| 10 | # Source0-md5: dc3543c14aa178d9f7a3fa4ee45fb43c | |
| 11 | URL: http://bioconductor.org/packages/release/bioc/html/%{packname}.html | |
| 12 | BuildRequires: R | |
| 13 | BuildRequires: R-Biobase | |
| 14 | BuildRequires: R-limma | |
| 15 | BuildRequires: R-affy | |
| 16 | BuildRequires: texlive-latex | |
| 17 | Requires: R | |
| 18 | Requires: R-Biobase | |
| 19 | Requires: R-limma | |
| 20 | Requires: R-affy | |
| 21 | BuildRoot: %{tmpdir}/%{name}-%{version}-root-%(id -u -n) | |
| 22 | ||
| 23 | %description | |
| 24 | The package implements a method for normalising microarray | |
| 25 | intensities, both between colours within array, and between arrays. | |
| 26 | The method uses a robust variant of the maximum-likelihood estimator | |
| 27 | for the stochastic model of microarray data described in | |
| 28 | the references (see vignette). The model incorporates data calibration | |
| 29 | (a.k.a. normalization), a model for the dependence of the variance on | |
| 30 | the mean intensity, and a variance stabilizing data transformation. | |
| 31 | Differences between transformed intensities are analogous to | |
| 32 | "normalized log-ratios". However, in contrast to the latter, their | |
| 33 | variance is independent of the mean, and they are usually more | |
| 34 | sensitive and specific in detecting differential transcription. | |
| 35 | ||
| 36 | %prep | |
| 37 | %setup -q -c -n %{packname} | |
| 38 | ||
| 39 | %build | |
| 40 | ||
| 41 | %install | |
| 42 | rm -rf $RPM_BUILD_ROOT | |
| 43 | install -d $RPM_BUILD_ROOT%{_libdir}/R/library | |
| 44 | ||
| 45 | R CMD INSTALL %{packname} -l $RPM_BUILD_ROOT%{_libdir}/R/library | |
| 46 | ||
| 47 | %clean | |
| 48 | rm -rf $RPM_BUILD_ROOT | |
| 49 | ||
| 50 | %files | |
| 51 | %defattr(644,root,root,755) | |
| 52 | %dir %{_libdir}/R/library/%{packname} | |
| 53 | %doc %{_libdir}/R/library/%{packname}/doc | |
| 54 | %doc %{_libdir}/R/library/%{packname}/html | |
| 55 | %doc %{_libdir}/R/library/%{packname}/DESCRIPTION | |
| 56 | %doc %{_libdir}/R/library/%{packname}/CITATION | |
| 57 | %{_libdir}/R/library/%{packname}/INDEX | |
| 58 | %{_libdir}/R/library/%{packname}/NAMESPACE | |
| 59 | %{_libdir}/R/library/%{packname}/Meta | |
| 60 | %{_libdir}/R/library/%{packname}/R | |
| 61 | %{_libdir}/R/library/%{packname}/help | |
| 62 | %{_libdir}/R/library/%{packname}/data | |
| 63 | %{_libdir}/R/library/%{packname}/scripts | |
| 64 | %dir %{_libdir}/R/library/%{packname}/libs | |
| 65 | %attr(755,root,root) %{_libdir}/R/library/%{packname}/libs/vsn.so |