A Protocol To Adopt The Mixture Model By Zhu Et Al. For The Analysis Of Population Stratification On The Data With Missing Allele Calls

There are two kinds of applications of principal component analysis (PCA) to analyze population substructures of genetic polymorphism data. One application is for an individual covariance matrix, and the other application is for a marker covariance matrix. The former method is already implemented in EIGENSTRAT 1; the latter method, however, is not common because it cannot be applied, if data include missing typing data (allele call). Here, we describe some modification of a Mixture Model...
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