SMA
Details
| Last Update: | 2008-02-15 11:01:51 |
| Version: | 1.2.0 |
| License/Program Type: | GPL (GNU General Public License) |
| Publisher: | Thomas Mailund |
| Price: | $0.00 |
Description:
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.
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SMA Version History
| Product |
Date Added |
| SMA 1.2.0 |
2008-02-15 11:01:51 |
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