MultiLociBiallelicModel

Author

Nicholas Hathaway

Published

December 11, 2023



Summary sheet

Main use-cases MOI;prevalence estimates
Authors Henri Christian Junior Tsoungui Obama;Kristan Alexander Schneider
Latest version NA
License MIT License
Website https://github.com/Maths-against-Malaria/MultiLociBiallelicModel
Code repository https://github.com/Maths-against-Malaria/MultiLociBiallelicModel
Publication https://www.frontiersin.org/articles/10.3389/fepid.2022.943625/full
Tutorial authors Nicholas Hathaway
Tutorial date 2023-12

Purpose

The code supplied by this paper does a maximum-likelihood (MLE) method to estimate:

  1. haplotype frequencies and prevalence
  2. multiplicity of infection (MOI/COI) from SNP data.

The functions here provide functionality to predict possible haplotype prevalence within the population that lead to the current set of data. Also estimates MOI/COI based on these estimates. Has to take only biallelic SNPs and compuationally can be limited by the number of loci supplied (in publication used 10 loci).

Existing resources

  • Example file can be found here

Citation

(Tsoungui Obama and Schneider 2022)

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References

Tsoungui Obama, Henri Christian Junior, and Kristan Alexander Schneider. 2022. “A Maximum-Likelihood Method to Estimate Haplotype Frequencies and Prevalence Alongside Multiplicity of Infection from SNP Data.” Frontiers in Epidemiology 2.