This github repo provides code and data to reproduce the results in "The impact of malaria-protective red blood cell polymorphisms on parasite biomass in children with severe Plasmodium falciparum malaria" by Uyoga et al (preprint).
This is a genetic case-only association study which uses parasite biomass as measured by the plasma concentration of PfHRP2 as a quantitative phenotype.
The raw data are given in the files kemri_case_data.csv (cases) and kemri_control_data.csv (controls). All the analysis can be reproduced by running the RMarkdown file PfHRP2_quantitative_trait.Rmd. This uses the following R packges:
- mitools (combine analyses on multiple imputation datasets)
- rstan (extract posterior samples from previously run model)
- mvtnorm (multivariate normal)
- matrixStats (useful functions such as logsumexp)
The main result compares the associations estimated in case-only analyses with three quantitative traits:
- peripheral parasite density
- plasma PfHRP2 concentration
- ratio of PfHRP2/parasite density
Any questions or if you spot any bugs please email me at jwatowatson at gmail dot com