coiaf

Introduction

In malaria, individuals are often infected with different parasite strains, with the complexity of infection (COI) giving the number of genetically different parasite strains in an individual. Changes in the mean COI in a population have been shown to be informative of changes in transmission intensity with a number of probabilistic likelihood and Bayesian models now developed to estimate COI. However, rapid, direct measures based on heterozygosity or FwS have not been directly related to the COI. In this package we present two new methods that use easily calculated measures to directly estimate the COI from sequence read depth data.

Installation

You may install the package from Github using devtools. You may either install the most recent release or the development version of the software.

# install.packages("devtools")

# Most recent release
devtools::install_github("bailey-lab/coiaf@v0.1.0")

# Development version
devtools::install_github("bailey-lab/coiaf")

Usage

Please consult the example real data vignette for a primer on how to run real data using coiaf. For a description of how the estimation methods work, please consult the example coi prediction vignette.

Development

Please note that this package is still under development and may be missing features.