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| Downloads: Statistical software |
| 1 GRIDHAPLO: a grid package for Genome Wide Haplotype Association Study (GWHAS) |
GridHaplo implements a sliding windows haplotype analysis approach for analyzing GWAS SNP data set as described in Tregouet et al. (see below complete reference).
GridHaplo is still under development but its beta version is available for download.
Tregouet DA, Konig IR, Erdmann J, Munteanu A, Braund PS, Hall AS, Grosshennig A, Linsel-Nitschke P, Perret C, Desuremain M, Meitinger T, Wright BJ, Preuss M, Balmforth AJ, Ball SG, Meisinger C, Germain C, Evans A, Arveiler D, Luc G, Ruidavets JB, Morrison C, van der Harst P, Schreiber S, Neureuther K, Schafer A, Bugert P, El Mokhtari NE, Schrezenmeir J, Stark K, Rubin D, Wichmann HE, Hengstenberg C, Ouwehand W, Ziegler A, Tiret L, Thompson JR, Cambien F, Schunkert H, Samani NJ. Genome-wide haplotype association study identifies the SLC22A3-LPAL2-LPA gene cluster as a risk locus for coronary artery disease. Nat Genet. 2009 Mar;41(3):283-5. Epub 2009 Feb 8. |
| License: - |
O/S: Linux/Windows |
Version: 1 |
| Added: 16.02.09 |
Downloads: 898 |
Download (3.4M) |
| 2 THESIAS - a new JAVA interface implementation (09/02/2007) |
*** INTRODUCTION***
The objectif of the THESIAS program is to performed haplotype-based association analysis
in unrelated individuals. This program is based on the maximum likelihood model described
in Tregouet et al. 2002 (Hum Mol Genet 2002,11: 2015-2023) and is linked to the SEM algorithm
(Tregouet et al. Ann Hum Genet 2004,68: 165-177).
THESIAS allows one to simultaneous estimate haplotype frequencies and their associated
effects on the phenotype of interest. In this new THESIAS release, quantitative, qualitative
(logistic and matched-pair analysis), categorical and survival outcomes can be studied.
X-linked haplotype analysis is also feasible.
Covariate-adjusted haplotype effects as well as haplotype x covariate interactions can also
be investigated.
Every information on how to run THESIAS and on what THESIAS do can be found in the Documentation.
This release now relies on a Java graphic Interface developped by Valerie Garelle.
*** SYSTEM REQUIREMENTS***
This new Java Interface version requires the Java Standard Edition Runtime Environment 1.4.2 (or more)
to be installed. For download please visit http://www.java.com/en/download/manual.jsp
and follow the Java Sun Instructions.
Even if it has been tested on Windows/Linux machines with 512Mo Ram capacity, a computer with at least
1Go memory is recommended.
*** INSTALLATION***
-For Windows:
After downloading the compressed file Thesias_3.1-win.zip , decompress it into any folder . This will
create a new folder called "Thesias_3.1-win" that will include the executable and the example data files.
To run Thesias, click on Thesias-3.1 or on Thesias_Debug. Using the latter allows one to display a black
window providing some informations about the running process of the program. It can be useful to check for
lack of convergence or incorrect use.
-For Linux:
After downloading the compressed file Thesias_3.1-linux.tar.gz, decompress it into any folder.
This will create a new folder called "Thesias_3.1-linux" that will include several files including
the example data files, a libthesiaslib.so and a Thesias.jar.
Copy the "libthesiaslib.so" into your /usr/lib folder (cp libthesiaslib.so /usr/lib/). For this, you need to be
logged in root user.
Back into the folder where THESIAS was decompressed, run THESIAS program by launching "java -jar Thesias.jar "
or equivalently "./Thesias_3.1.sh "
*** CAUTION ***
Running THESIAS will create 5 files (paramData.thi,para.txt,result.htm, result.txt and datafile.txt).
The first two must not be modified.
The result.htm and result.txt correspond to the output of the current run.
Feel free to contact DA Tregouet at tregouet@chups.jussieu.fr for any help, information and reporting bugs.
*** REFERENCE ***
Tregouet DA, Garelle V. A new JAVA interface implementation of THESIAS: Testing Haplotypes EffectS In Association Studies. Bioinformatics. 2007;23(8):1038-1039.
**************************************************
|
| License: |
O/S: PC/Linux/Sun |
Version: 3.1 |
| Added: 11.05.07 |
Downloads: 3389 |
Download () |
| 3 THESIAS 27/03/2006 |
The THESIAS program
"Testing Haplotype Effects In Association Studies"
by Tregouet David-Alexandre (david.tregouet@chups.jussieu.fr)
INSERM U525,
Genetic Epidemiology and Molecular of Cardiovascular Pathologies
Paris, France
/*THESIAS program was updated on Tuesday 21st february 2006 :
Haplotype analysis of a categorical phenotype is now possible by use of a polytomous formulation.
Besides, X-linked SNPs analysis is now available for case-control and quantitative analysis.
*/
**************************************************************************************************
The objectif of the THESIAS program is to performed haplotype-based association analysis
in unrelated individuals. This program is based on the maximum likelihood model described
in Tregouet et al. 2002 and is linked to the SEM algorithm (Tregouet et al. 2004).
THESIAS allows the simultaneous estimation of haplotype frequencies and of their associated
effects on the phenotype of interest. In its current version, quantitative, qualitative, categorical
and survival outcome can be studied.
Covariate-adjusted haplotype effects as well as haplotype x covariate interactions can
be investigated.
Every information on how to run THESIAS and on what THESIAS do can be found in the Documentation3.1.htm File.
In order to illustrate the use of the THESIAS program, several .txt and .html files are available
for download through the example.zip file.
**************************************************************************************************
The Data.txt file includes one quantitative phenotype (in position 2),two polymorphisms
(in position 3 and 4) and two additional covariates (in position 5 and 6).
In the Answer0.txt file are given the appropriate responses to be given to THESIAS in order to get
the parameter file (para.txt). The results files should then be similar to para0.txt, result0.txt
and result0.htm
In the Answer1.txt file are given the appropriate responses to be given to THESIAS in order to get
the loglikelihood of a model testing the effect of the two covariates on the phenotype but with no
haplotype effects. The results files should then be similar to result1.txt and result1.htm .
If one wants to further estimate haplotype effects, para.txt must have to be modified as in para1.txt .
Then run the THESIAS program with the responses given in the answer2.txt file. The results files should
then be similar to result2.txt and result2.htm .
**************************************************************************************************
In order to illustrate the use of the extended THESIAS program for survival outcome analysis,
several .txt files are available for download through the example2.zip file.
The data.dat file includes one censored phenotype (in position 3) with its associated survival time
(in position 4),six polymorphisms (in position 5 to 10) and three additional covariates
(in position 11 to 13).
In the Answer0.txt file are given the appropriate responses to be given to THESIAS in order to get
the parameter file (para.txt). The results files should then be similar to para0.txt, result0.txt
In the Answer1.txt file are given the appropriate responses to be given to THESIAS in order to get
the loglikelihood of a model testing the effects of the five most frequent haplotypes. The results file
should then be similar to result1.txt.
**************************************************************************************************
|
| License: |
O/S: PC/Linux/Sun |
Version: 3.1 |
| Added: 27.03.06 |
Downloads: 2813 |
Download () |
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