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The treeWAS R package allows users to apply our phylogenetically-informed Genome-Wide Association Studies (GWAS) approach to microbial genetic and phenotypic data. In short, treeWAS measures the statistical association between a phenotype of interest and the genotype at all loci, with the aim of identifying significant associations, while correcting for the confounding effects of clonal population structure and homologous recombination. treeWAS is applicable to both bacterial and viral genetic data from both the core and accessory genomes, and to binary, continuous, and categorical phenotypes.
treeWAS is currently hosted on GitHub at https://github.com/caitiecollins/treeWAS.
The most up-to-date version of treeWAS can be easily installed directly within R, using the devtools package:
## install devtools, if necessary:
install.packages("devtools", dep=TRUE)
library(devtools)
## install treeWAS from github:
install_github("caitiecollins/treeWAS", build_vignettes = TRUE)
library(treeWAS)
To open the vignette from within R (recommended if any formatted elements are not rendering properly where you are currently reading this),
run browseVignettes and click on the HTML hyperlink:
browseVignettes("treeWAS")
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Click on the links in this page's sidebar to access the treeWAS documentation you're looking for.