SMA

SMA software is a collection of programs that are specifically designed to perform various tests for association between genotypes at a single marker and a binary disease status. There are some requirements for installing and using this software, including Boost, GSL and SNPfile.

Installation is simple and straightforward. Firstly, you need to "cd" to the directory containing the program's source code and type "./configure" to configure the package for your system. During this process, you will receive messages that indicate the features it is checking for, but it may take a while to complete.

Secondly, you will need to type "make" to compile the package. If you want to run self-tests that come with the package, you can opt to type "make check". Once compiled, you can install the programs, data files and documentation by typing "make install". Lastly, to remove program binaries and object files from the source code directory, you can delete them by typing "make clean".

At present, the programs can only read input files in the SNPfile format. The meta data protocol is required and it includes positions in a std::vector containing the position for each marker. Phenotypes are ordered in the same way as the rows in the genotype matrix, and markerNames are in a std::vector containing string IDs for the marker. This meta data protocol is used for case/control data by the snp_file_convert program in the SNPfile package.

In this release, the version has been updated with a port to the SNPFile version 2.0 format. Overall, SMA software is an efficient and reliable tool for carrying out genetic association tests.