SEAGLE Package for R

An R package for Large-Scale Set-Based Gene-Environment Interaction Tests in Biobank Data

About the package

The SEAGLE package for R is software for Large-Scale Set-Based Gene-Environment Interaction Tests in Biobank Data. The package is available on CRAN at https://CRAN.R-project.org/package=SEAGLE and on GitHub at https://jocelynchi.github.io/SEAGLE/.

Data for Tutorials in Examples 3 and 4

The example GWAS and next generation sequencing data for Example 3 at https://jocelynchi.github.io/SEAGLE/ can be downloaded from http://jocelynchi.com/SEAGLE/SEAGLE-example3-data.zip.

The example GWAS data from chromosome 22 for Example 4 at https://jocelynchi.github.io/SEAGLE/ can be downloaded from http://jocelynchi.com/SEAGLE/SEAGLE-example4-data.zip.

Many thanks to Yueyang Huang for generating the example GWAS and next generation sequencing data and the PLINK1.9 code for these tutorials.

Citing SEAGLE

The accompanying journal manuscript for the SEAGLE package can be found online here. To cite the SEAGLE software, please use the following BibTeX entry.

@article{seagle,
  author = {Jocelyn T. Chi and Ilse C. F. Ipsen and Tzu-Hung Hsiao and Ching-Heng Lin and Li-San Wang and Wan-Ping Lee and Tzu-Pin Lu and Jung-Ying Tzeng},
  title = {SEAGLE: A Scalable Exact Algorithm for Large-Scale Set-Based Gene-Environment Interaction Tests in Biobank Data},
  year = {2021},
  arxiv = {https://arxiv.org/abs/2105.03228},
  journal = {Frontiers in Genetics, section Statistical Genetics and Methodology},
  volume = {12},
  pages = {1878},
  pdf = {https://www.frontiersin.org/articles/10.3389/fgene.2021.710055/pdf},
  code = {http://jocelynchi.com/SEAGLE},
  doi = {10.3389/fgene.2021.710055},
  link = {https://www.frontiersin.org/articles/10.3389/fgene.2021.710055/full}
}