The SMR software tool was originally developed to implement the SMR & HEIDI methods to test for pleiotropic association between the expression level of a gene and a complex trait of interest using summary-level data from GWAS and expression quantitative trait loci (eQTL) studies (Zhu et al. 2016 Nature Genetics). The SMR & HEIDI methodology can be interpreted as an analysis to test if the effect size of a SNP on the phenotype is mediated by gene expression. This tool can therefore be used to prioritize genes underlying GWAS hits for follow-up functional studies. The methods are applicable to all kinds of molecular QTL (xQTL) data, including DNA methylation QTL (mQTL) and protein abundance QTL (pQTL).
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Eigen
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libz
Install Eigen and libz. If you want build smr staticlly, you need static library of those them. And the static version of omp is needed too.
Simply, in smr directoy,
make
If you want compile static version, type:
make smr_static
If your Eigen or libz is not installed in standard head file and library searching path, you can specific them as following:
make EIGEN_PATH="where the Eigen's head file located" ZLIB_INCLUDE="path of zlib head file" ZLIB_LIB="path of zlib library"
To build smr by debug mode, using:
make DEBUG=ON
In SMR directory,
mkdir build
cd build
cmake ..
makeTo turn on debug,
cmake -DCMAKE_BUILD_TYPE=DEBUG ..To build static version of SMR,
cmake -DBUILD_STATIC=ON ..If you need specify Eigne path you can use -Deigen_path="path_to_Eigen" when run cmake ... To specify zlib head and library files, using -Dzlib_path=path_to_your_zlib. If your zlib head file and library located in different directory, you can use -Dzlib_include_path=where_zlib_head_files and -Dzlib_lib_path=where_zlib_lib to specify them.
visit https://yanglab.westlake.edu.cn/software/smr/ for software's document.