SMA

SMA consists of a small collection of programs that performs different tests for association between genotypes at a single marker and a binary disease status.

SMA is released under the GNU General Public License.

SMA is written in C++ and is available as source code (under the GNU General Public License, GPL). and as binary versions as Linux RPM files. The source code has been successfully compiled on various Linux systems. As I have only limited access to architectures other than Linux, it is not possible for me to make binary distributions for other platforms, but if anyone is willing to build the distributions I will be more than happy to put them on this site.

SMA requires the Boost Library, the GNU Scientific Library (GSL), and the SNPfile library to be installed.

• Boost can be obtained from http://www.boost.org.
• GSL can be obtained from http://www.gnu.org/software/gsl/.
• SNPfile can be obtained from http://www.birc.au.dk/~mailund/SNPfile/index.html.

The most recent versions of SMA can be downloaded below, older versions are available from here.

Binary Distributions

• sma-1.2.1-1.i386.rpm
• sma-1.2.0-1.i386.rpm
• sma-1.1.0-1.i386.rpm
• sma-1.0.0-1.i386.rpm

• sma_1.2.1_i386.deb
• sma_1.2.0_i386.deb
• sma_1.2.0_amd64.deb
• sma_1.1.0_i386.deb

The rpm-files were built on Linux Fedora Core 5. The Debian files were built on Ubuntu Feisty Fawn. If you have problems installing these files on other Redhat or Debian based systems, please let me know.

Source Code Distributions

• sma-1.2.1.tar.gz
• sma-1.2.0.tar.gz
• sma-1.1.0.tar.gz
• sma-1.0.0.tar.gz
• sma-0.9.0.tar.gz (beta release)

To build the source files, first uncompress and untar the file, then run 'configure' and finally 'make'. To test that the build was successful, run 'make check'. To install the program, run 'make install'.

    $ tar zxf sma-version.tar.gz
    $ cd sma-version
    $ ./configure
    $ make
    $ make check
    $ make install

Currently, the programs only read input files in the SNPfile format. In this format, the meta data protocol is:

• positions is a std::vector<int> containing the position for each marker, in the same order as genotype columns are ordered in the genotype matrix.
• phenotypes is, for case/control data a std::vector<bool> containing the binary disease status (true for diseased, false for not diseased) for each individual, ordered in the same order as the rows in the genotype matrix. For QTL mapping, it is a std::vector<double> with a floating point value for each individual.
• markerNames is a std::vector<std::string> containing string IDs for each marker, in the same order as genotype columns are ordered in the genotype matrix.

This is the same meta data protocol as used by the snp_file_convert program in the SNPfile package and by the Blossoc tool and for the case/control format by the HapCluster tool.

We hope to have a users' manual available soon.

Programs

• chisq_sma — A χ²-test for association (2x2 or 2x3 contingency tables, depending on whether the test is a genotype or allele test).
• beta_sma — A Bayesian association test based on ideas from A tutorial on statistical methods for population association studies. D.J. Balding. Nat Rev Genet 2006 7(10), 781–791.
• F-test_sma — An F-test for genotype association between a marker and a quantitative trait. At the allelic level it performs a t-test.

For bug-reports or feature requests, please use our bug-tracking software.

For comments or questions, please contact Thomas Mailund <mailund@birc.au.dk>, Bioinformatics Research Center (BiRC), University of Aarhus, Høegh-Guldbergsgade 10, DK-8000 Århus C.