PSMIX: an R package for population structure inference via maximum likelihood method

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 multiloc...

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Bibliographic Details
Published in:BMC bioinformatics 2006-06, Vol.7 (1), p.317-317, Article 317
Main Authors: Wu, Baolin, Liu, Nianjun, Zhao, Hongyu
Format: Article
Language:English
Subjects:
Algorithms
American Indian or Alaska Native - genetics
Bayes Theorem
Chromosome Mapping - methods
Computer Simulation
Genetics, Population - methods
Humans
Likelihood Functions
Models, Genetic
Software
White People - genetics
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Summary: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. We have developed PSMIX, an R package based on maximum likelihood method using expectation-maximization algorithm, for inference of population stratification and individual admixture. 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.
ISSN:1471-2105
1471-2105
DOI:10.1186/1471-2105-7-317