caravagn / mtree

Mutation tree from binary bulk sequencing data

mtree

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 with probabilistic causation.

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. 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.

mtree is part of the evoverse, a set of R packages to implement Cancer Evolution analyses.

Help and support

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Installation

You can install the released version of mtree from GitHub with:

# install.packages("devtools")
devtools::install_github("caravagn/mtree")

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Copyright and contacts

Giulio Caravagna, PhD. Institute of Cancer Research, London, UK.

• Personal webpage: https://bit.ly/2kc9E6Y,
• Email address: [e-mail] and [e-mail]
• Twitter feed: @gcaravagna
• GitHub space: caravagn