Markov chain Monte Carlo Gibbs sampler approach for estimating haplotype frequencies among multiple malaria infected human blood samples

Table 3 The mean squared error (MSE) of the estimated haplotype frequencies with simulated population and sample haplotype frequencies across statistical methods and four conditions of LoD_SNP (30%, 20%, 10%, 0%) and LoD_MOI (15%, 10%, 5%, 0%)

	MHF	R-EM	Bayesian	EM	MCMC	Gibbs
Population haplotype (LoD_SNP/LoD_MOI)
0/0	0.103	0.178	0.091	0.050	0.085	0.097
0.10/0.05	0.108	0.138	0.088	0.043	0.047	0.065
0.20/0.10	0.120	0.103	0.108	0.051	0.040	0.050
0.30/0.15	0.177	0.086	0.141	0.072	0.076	0.062
Sample haplotype (LoD_SNP/LoD_MOI)
0/0	0.082	0.158	0.077	0.041	0.080	0.091
0.10/0.05	0.086	0.117	0.072	0.032	0.038	0.055
0.20/0.10	0.095	0.081	0.089	0.036	0.027	0.037
0.30/0.15	0.150	0.063	0.122	0.053	0.058	0.044

Lower value represents higher accuracy
MHF MalHaploFreq, R-EM malaria em, Bayesian Bayesian statistic, EM EM algorithm, MCMC Markov chain Monte Carlo, Gibbs Gibbs sampler, LoD limit of detection, SNP single nucleotide polymorphisms, MOI multiplicity of infection

ISSN: 1475-2875