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fGWAS: Functional GWAS software (Version 2.0)


The fGWAS (Function Genome-wide association study) is a new concept to evaluate additive and dominant effect for every SNP and identify the significant SNPs from huge SNP data. Since R. Wu[1] et al. put forward this new concept, 3 statistical models have been developed to find the relationship between SNP data and the longitudinal traits, including Bayesian Lasso[2], Bayesian Group Lasso[3] and dynamic model[4].

The fGWAS software aims at building a general platform to analyse SNP data with longitudinal trails. This platform provides multiple statistical models and uniform interface to the end-users. We develop this software in C/C++ to gain fast speed and more compatibility with main computing platform. The details will be described in the section 5 and in the introduction document.

So far the fGWAS software implements four statistical models, MLREG, DYNMODEL, BLASSO and GLASSO model.

They have same statistical models as R/fGWAS2. Please visit R/fGWAS2 to get the details.
Here we refer to the following publications for the theoretical foundation of this software. If you appreciate this software then please cite the following papers in your work.

[1]: Jiangtao Luo, Arthur Berg, Kwangi Ahn, Kiranmoy Das, Jiahan Li, Zhong Wang, Yao Li, Rongling Wu. Functional genome-wide association studies of longitudinal traits. In: Handbook of Adaptive Designs in Pharmaceutical and Clinical Development 2010, edited by S. C. Chow. Wiley, London, UK.

[2]: Kiranmoy Das, Jiahan Li, Zhong Wang, Chunfa Tong, Guifang Fu, Yao Li, Meng Xu, Kwangmi Ahn, David Mauger and Runze Li, et al. A dynamic model for genome-wide association studies . Human Genetics(2011) doi: 10.1007/s00439-011-0960-6

[3]: Jiahan Li, Kiranmoy Das, Guifang fu, Runze Li and Rongling Wu. The Bayesian Lasso for Genome-wide Associations Studies. Bioinformatics (2011) 27 (4): 516-523. doi: 10.1093/bioinformatics/btq688

[4]: Jiahan Li, Runze Li, and Rongling Wu. Bayesian Group LASSO for Varying-Coefficient Models With Application to Functional Genome-Wide Association Studies.


The software for Windows OS is available now. We are planning to release the versions for the LINUX and Mac. The document also can be downloaded by the following link.

  • Introduction for the fGWAS software.(Coming soon)
  • Windows OS (10/05/2012, 3.58 MB)
  • Source (10/05/2012, 697 KB)


It is easy to install this software in the Windows, just download the setup file and extract into a folder. The 4 commands are available in the DOS command windows.
  • mlreg.exe
  • blasso.exe
  • dynmodel.exe
  • glasso.exe
In the Unix/Linux or other clusters, the program need to be compiled from R package. The source is compatible with R-2.12.0. We don't test it in other R environment. Please be careful to transportation the source. Here provides a full package of R 2.12.0. Based on this R environment, fGWAS software can be compiled in the Linux/Unix.

Update History:

10/05/2012: Version 2.0 is released.
03/03/2011: Version 1.0 is released.

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