katiesaund/hogwash: Three Bacterial Genome-Wide Association Study Methods

Three methods to identify genetic loci associated with either a binary (two methods) or continuous phenotype (one method) while controlling for the clonal nature of the bacterial population. A feature of this package is the ability to group together related genotypes to increase the power to detect a relationship between the genotype and the phenotype of interest. The three methods all depend on convergence in both the phenotype and genotype to coincide on edges of the phylogenetic tree. The three methods are the Continuous Test, the Synchronous Test, and PhyC. This package's PhyC method is an implementation of the bacterial GWAS method originally described in Farhat et al. (2013) <doi.org/10.1038/ng.2747>.

install.packages("remotes")
remotes::install_github("katiesaund/hogwash")