Multiplicity of Infection and Allele Frequency Recovery from Noisy Polyallelic Genetics Data

A Markov Chain Monte Carlo (MCMC) based approach to Bayesian estimation of individual level multiplicity of infection, within host relatedness, and population allele frequencies from polyallelic genetic data. Implements the model described in Murphy and Greenhouse (2024) .

moire

moire is a package implementing an MCMC based approach to estimating complexity of infection (COI), also sometimes referred to as multiplicity of infection (MOI), population allele frequencies, and within-host relatedness from polyallelic genomics data.

Installation

moire can be installed either using our r-universe repository (preferred)

# Install from r-universe
install.packages("moire", repos = c("https://eppicenter.r-universe.dev", "https://cloud.r-project.org"))

or from GitHub using remotes

# Install development version from Github
remotes::install_github("EPPIcenter/moire")

Usage

moire supports loading data from either a long format data.frame using load_long_form_data() or from a wide format data.frame using load_delimited_data().

df <- read.csv("your_data.csv")
data <- load_long_form_data(df)

# With data in appropriate format, run MCMC as follows
mcmc_results <- moire::run_mcmc(data, is_missing = data$is_missing, seed = 1)

Manuscript

The paper describing our method may be found here