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After globalMPRRefine, you should use Bayes to call final genotype.
genotypeCallsBayes(ALLELE.num, errorRate = 5e-04, eps = 1e-10, maxIterate = 100, verbose = FALSE)
one result of globalMPRRefine
errorRate
eps
maxIterate to control running time
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globalMPRRefine
# NOT RUN { ALLELE.num=matrix(c(100,1, 50,55, 89,2, 1,101, 0,78),5,3,byrow=TRUE) genotypeCallsBayes(ALLELE.num) # }
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