SMA 1.2.0

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

Requirements:

Boost
GSL
SNPfile

Installation:

The simplest way to compile this package is:

1. `cd' to the directory containing the package's source code and type
`./configure' to configure the package for your system. If you're
using `csh' on an old version of System V, you might need to type
`sh ./configure' instead to prevent `csh' from trying to execute
`configure' itself.

Running `configure' takes awhile. While running, it prints some
messages telling which features it is checking for.

2. Type `make' to compile the package.

3. Optionally, type `make check' to run any self-tests that come with
the package.

4. Type `make install' to install the programs and any data files and
documentation.

5. You can remove the program binaries and object files from the
source code directory by typing `make clean'. To also remove the
files that `configure' created (so you can compile the package for
a different kind of computer), type `make distclean'. There is
also a `make maintainer-clean' target, but that is intended mainly
for the package's developers. If you use it, you may have to get
all sorts of other programs in order to regenerate files that came
with the distribution.

Usage:

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 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.

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 for case/control data by the snp_file_convert program in the SNPfile package.

What's New in This Release:

This version is a port to the SNPFile version 2.0 format.

last updated on:
February 15th, 2008, 10:29 GMT
price:
FREE!
homepage:
www.daimi.au.dk
license type:
GPL (GNU General Public License) 
developed by:
Thomas Mailund
category:
ROOT \ Science and Engineering \ Medical Science Apps.
SMA
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