Markov chain Monte Carlo and expectation maximization approaches for estimation of haplotype frequencies for multiply infected human blood samples

Table 2 The haplotype frequency estimations for real data set (Swiss TPH), n = 82 individual

SNP 1	SNP 2	MHF	R-EM	Bayesian	EM	MCMC
1	1	0.928 (0.892–0.955)	0.914 (0.858–0.970)	0.936 (0.907–0.960)	0.908 (0.821–0.961)	0.914 (0.828–0.965)
1	2	0.011 (0.002–0.030)	0.016 (0.000–0.041)	0.017 (0.006–0.037)	0.013 (0.000–0.070)	0.021 (0.002–0.083)
2	1	0.004 (0.000–0.017)	0.005 (0.000–0.018)	0.007 (0.001–0.017)	0.009 (0.000–0.064)	0.008 (0.000–0.061)
2	2	0.057 (0.033–0.089)	0.065 (0.008–0.121)	0.038 (0.017–0.064)	0.069 (0.024–0.150)	0.058 (0.017–0.135)

SNP 1 = wildtype alone, 2 = mutant alone, MHF MalHaploFreq, R-EM malaria.em, Bayesian Bayesian statistic, EM EM algorithm, MCMC Markov chain Monte Carlo

ISSN: 1475-2875