# treeWAS

**Repository Path**: sheng0825/treeWAS

## Basic Information

- **Project Name**: treeWAS
- **Description**: No description available
- **Primary Language**: Unknown
- **License**: Not specified
- **Default Branch**: master
- **Homepage**: None
- **GVP Project**: No

## Statistics

- **Stars**: 0
- **Forks**: 0
- **Created**: 2021-05-10
- **Last Updated**: 2021-05-10

## Categories & Tags

**Categories**: Uncategorized

**Tags**: None

## README

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# *treeWAS*: A phylogenetic tree-based approach to genome-wide association studies in microbes


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## Introduction
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The *treeWAS* R package allows users to apply our phylogenetic tree-based appraoch to Genome-Wide Association Studies (GWAS) 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 both binary and continuous phenotypes.The approach adopted within *treeWAS* is described fully in our paper, available in [PLOS Computational Biology](http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005958).



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## Installation
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*treeWAS* is currently hosted on GitHub at <https://github.com/caitiecollins/treeWAS>.  
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The most up-to-date version of *treeWAS* can be easily installed directly within R, using the `devtools` package: 


```{r, eval=FALSE, highlight=TRUE}
## install devtools, if necessary:
install.packages("devtools", dep=TRUE)
library(devtools)

## install treeWAS from github:
install_github("caitiecollins/treeWAS", build_vignettes = TRUE)
library(treeWAS)
```


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## Documentation
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Documentation on how to use *treeWAS* can be found on GitHub in [the Wiki](https://github.com/caitiecollins/treeWAS/wiki). 


The Wiki contains sections on [The Method](https://github.com/caitiecollins/treeWAS/wiki/1.-How-treeWAS-Works) behind *treeWAS*, 
the [Data & Data Cleaning](https://github.com/caitiecollins/treeWAS/wiki/2.-Data-&-Data-Cleaning) required, 
the [treeWAS Function & Arguments](https://github.com/caitiecollins/treeWAS/wiki/3.-treeWAS-Function-&-Arguments), 
a guide to [Interpreting Output](https://github.com/caitiecollins/treeWAS/wiki/4.-Interpreting-Output) returned by *treeWAS*, 
functions to facilitate [Integration with ClonalFrameML](https://github.com/caitiecollins/treeWAS/wiki/5.-ClonalFrameML-Integration), 
and information describing how to flag [Bugs & Features](https://github.com/caitiecollins/treeWAS/wiki/6.-Bugs-&-Features).



Once you have installed and loaded the *treeWAS* package, you can also find this information in the vignette. 
To open the vignette from within R (recommended if any formatted elements are not rendering properly in the wiki), 
run `browseVignettes` and click on the `HTML` hyperlink:


```{r, eval=FALSE}
browseVignettes("treeWAS")
```

You may also find useful tips and relevant discussions among the [Issues](https://github.com/caitiecollins/treeWAS/issues) posted by other users (including [Closed Issues](https://github.com/caitiecollins/treeWAS/issues?q=is%3Aissue+is%3Aclosed)).


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