PSMIX: an R package for population structure inference via maximum likelihood method. Background: Inference of population stratification and individual admixture from genetic markers is an integrative part of a study in diverse situations, such as association mapping and evolutionary studies. Bayesian methods have been proposed for population stratification and admixture inference using multilocus genotypes and widely used in practice. However, these Bayesian methods demand intensive computation resources and may run into convergence problem in Markov Chain Monte Carlo based posterior samplings. Results: We have developed PSMIX, an R package based on maximum likelihood method using expectation-maximization algorithm, for inference of population stratification and individual admixture. Conclusion: Compared with software based on Bayesian methods (e.g., STRUCTURE), PSMIX has similar accuracy, but more efficient computations. PSMIX and its supplemental documents are freely available at http://bioinformatics.med.yale.edu/PSMIX
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References in zbMATH (referenced in 4 articles )
Showing results 1 to 4 of 4.
- de los Campos, Gustavo; Veturi, Yogasudha; Vazquez, Ana I.; Lehermeier, Christina; Pérez-Rodríguez, Paulino: Incorporating genetic heterogeneity in whole-genome regressions using interactions (2015)
- Liu, Nianjun; Zhao, Hongyu; Patki, Amit; Limdi, Nita A.; Allison, David B.: Controlling population structure in human genetic association studies with samples of unrelated individuals (2011)
- Bingham, Ella; Mannila, Heikki: Complexity control in a mixture model by the Hardy-Weinberg equilibrium (2009)
- Vaughan, Laura K.; Divers, Jasmin; Padilla, Miguel A.; Redden, David T.; Tiwari, Hemant K.; Pomp, Daniel; Allison, David B.: The use of plasmodes as a supplement to simulations: a simple example evaluating individual admixture estimation methodologies (2009)