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README.Rmd
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README.Rmd
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---
output: github_document
---
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
```
# mtree <a href='https://caravagn.github.io/mtree/'> <img src='man/figures/logo.png' align="right" height="139" /> </a>
<!-- badges: start -->
[](https://travis-ci.org/caravagn/mtree)
[](https://www.tidyverse.org/lifecycle/#maturing)
[](https://caravagn.github.io/evoverse)
<!-- badges: end -->
Thee `mtree` package provides a simple implementation of *mutation trees* in cancer.
Mutation trees can be built from binary data reporting the presence or absence of specific mutations - or any other somatic covariates - across a number of tumour regions. In this `mtree`, we integrate [Chow-Liu trees](https://en.wikipedia.org/wiki/Chow%E2%80%93Liu_tree) with [probabilistic causation](https://plato.stanford.edu/entries/causation-probabilistic/).
This type of models can be used to study the evolutionary trajectories of a tumour from bulk sequencing data, especially in setups where only targeted sequencing panels are available and methods for subclonal deconvolution cannot be used.
* `mtree` provides an S3-based implementation of mutation trees, as well as a Monte Carlo sampler that has been discussed in [Caravagna et al; PMID: 30171232](https://www.ncbi.nlm.nih.gov/pubmed/30171232). The package provides also functions to plot and analyze the trees.
* The sibling of a mutation tree is a *clone tree*, which is obtained from subclonal deconvolution of bulk samples when whole-genome/ exome sequencing is available; clone trees are implemented in the [ctree package](https://caravagn.github.io/ctree).
`mtree` is part of the `evoverse`, a [set of R packages](https://caravagn.github.io/evoverse) to implement Cancer Evolution analyses.
#### Help and support
[](https://caravagn.github.io/mtree)
-----
### Installation
You can install the released version of `mtree` from
[GitHub](https://github.com/) with:
``` r
# install.packages("devtools")
devtools::install_github("caravagn/mtree")
```
-----
#### Copyright and contacts
Giulio Caravagna, PhD. _Institute of Cancer Research, London, UK_.
[](mailto:gcaravagn@gmail.com)
[](https://github.com/caravagn)
[](https://twitter.com/gcaravagna)
[](https://sites.google.com/site/giuliocaravagna/)