Installation

mtPGS is implemented as a C++ package, which can be installed from GitHub by:

Dependencies #

• C++ library: Armadillo
• Statistical genetics software: PLINK

1. Install Armadillo if necessary #

Armadillo is a C++ library for linear algebra and scientific computing. Before installing Armadillo package, please ensure CMake tool, LAPACK and BLAS (or preferably OpenBLAS) are installed on your system. If these tools are not installed, you can download them from http://www.cmake.org (CMake tool) and http://www.openblas.net/ (OpenBLAS library). If you prefer to install the library and headers for Armadillo package in a user’s own directory, please use the option CMAKE_INSTALL_PREFIX as follows.

wget http://sourceforge.net/projects/arma/files/armadillo-9.200.7.tar.xz
tar xf armadillo-9.200.7.tar.xz
cd armadillo-9.200.7
cmake . -DCMAKE_INSTALL_PREFIX:PATH=/xxxx/armadillo-9.200.7
make && make install

2. Install mtPGS #

git clone https://github.com/xuchang0201/mtPGS.git
cd mtPGS/src
make

3. Check the options included in the mtPGS #

./mtPGS_int_ext -h #check input options for mtPGS that takes four sets of summary statistics 
./mtPGS_int_only -h #check input options for mtPGS that takes two sets of summary statistics