EIGENSOFT package combines functionality from our population genetics methods (Patterson et al. 2006) and our EIGENSTRAT stratification method (Price et al. 2006). The EIGENSTRAT method uses principal components analysis to explicitly model ancestry differences between cases and controls along continuous axes of variation; the resulting correction is specific to a candidate marker’s variation in frequency across ancestral populations, minimizing spurious associations while maximizing power to detect true associations. The EIGENSOFT package has a built-in plotting script and supports multiple file formats and quantitative phenotypes.
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Nature Genetics 38, 904 – 909 (2006) Published online: 23 July 2006; | doi:10.1038/ng1847
Principal components analysis corrects for stratification in genome-wide association studies
Alkes L Price, Nick J Patterson, Robert M Plenge, Michael E Weinblatt, Nancy A Shadick & David Reich
Population Structure and Eigenanalysis
Nick Patterson, Alkes L. Price, David Reich
December 2006 Issue of PLoS Genetics