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

Table 4 The average change coefficient (C) of the estimated haplotype frequencies with simulated population and sample haplotype frequencies for haplotype frequency > 5% 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	20.8	25.2	18.7	13.2	17.7	16.1
0.10/0.05	19.3	22.3	18.0	12.4	13.4	13.7
0.20/0.10	19.8	19.7	18.6	13.0	11.9	12.9
0.30/0.15	22.0	17.8	20.1	14.6	14.4	14.4
Sample haplotype (LoD_SNP/LoD_MOI)
0/0	18.8	23.7	17.4	12.0	17.2	15.4
0.10/0.05	17.0	20.5	16.3	10.9	12.4	12.5
0.20/0.10	17.7	17.5	17.1	11.4	10.4	11.3
0.30/0.15	20.6	15.4	18.8	13.0	13.1	12.8

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