DESCRIPTION

Package: hogwash
Type: Package
Title: Three Bacterial Genome-Wide Association Study Methods
Version: 1.2.5
Author: Katie Saund <katiephd@umich.edu>
Maintainer: Katie Saund <katiephd@umich.edu>
Description: 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>. 
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Imports: 
    ape,
    graphics,
    grDevices,
    pheatmap,
    phytools,
    stats,
    utils,
    methods,
    caper,
    scales
Suggests: 
    testthat,
    knitr,
    rmarkdown,
    covr
VignetteBuilder: knitr
RoxygenNote: 7.1.0
URL: https://github.com/katiesaund/hogwash/wiki
Depends: R (>= 3.6.0)