| Main use-cases | Frequency/prevalence estimation of phased genotypes |
| Authors | Aimee Taylor |
| Latest version | |
| License | MIT |
| Website | NA |
| Code repository | https://github.com/aimeertaylor/FreqEstimationModel |
| Publication | https://doi.org/10.1186/1475-2875-13-102 |
| Tutorial authors | TODO |
| Tutorial date | TODO |
FreqEstimationModel
Summary sheet
Purpose
The FreqEstimationModel R package estimates population-level frequencies of genetic markers of antimalarial resistance where
- genetic markers of antimalarial resistance are either alleles at single biallelic SNPs or sequences of alleles (haplotypes) over a small number of biallelic SNPs (at most seven) in the malaria parasite genome;
- population-level parasite frequencies (vs within-infection parasite frequencies) are estimated by jointly modelling parasite genetic data on many infections, including those that contain genetically distinct parasites (i.e., those that are polyclonal);
- parasite genetic data are prevalence data (i.e., they describe the presence of alleles). A non-default version of the model does exploit information on read-depths (see note on chapter 6 below), but it has not been peer-reviewed.
Existing resources
The FreqEstimationModel GitHub repository includes scripts for implementing FreqEstimationModel as well as vignettes demonstrating usage.
Citation
The publications associated with the FreqEstimationModel can be found at: