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Three bacterial GWAS methods all rolled into one easy-to-use R package
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README.md
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README.md

Summary

The hogwash R package is a phylogenetically-informed, convergence-based method for performing genome-wide association studies in bacteria. In short, the user inputs a phylogenetic tree, a phenotype (either binary or continuous), and a genotype (a binary matrix) and receives an output of the genotypes that are significantly associated with the phenotype after correcting for multiple testing, requiring convergence, and accounting for the clonal structure of the population.

Install the package

install.packages("devtools")
devtools::install_github("katiesaund/hogwash")
library(hogwash)

Getting started

Please check out the wiki for a brief primer on bacterial GWAS, detailed descriptions of the algorithms, and example data with results.

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