denovolyzeR

denovolyzeR is an R package for the analysis of de novo (sporadic) genetic variants, using a statistical framework described and validated by Samocha et al. Briefly, for each gene we derive the expected number of de novo events in a given population based on the mutability of the gene and the number of individuals sequenced, compare the observed number of de novos against expectation using a Poisson framework, and determine whether there is an excess of de novo events in a given variant class, gene, or pathway.

This approach has been applied to explore the role of de novo variants in a number of contexts, including autism spectrum disorders (Samocha et al Nature Genetics 2014) and congenital heart disease (Homsy et al Science 2015).

If using this software, please cite:
Curr Protoc Hum Genet. 2015;87:7.25.1-15. doi: 10.1002/0471142905.hg0725s87.

For a worked example of a typical de novo analysis using denovolyzeR, see the denovolyzeR package vignette.

Installation

The latest released version can be installed from CRAN:

install.packages("denovolyzeR")

The latest development version can be installed from GitHub. One simple approach uses devtools:

## Install devtools if not already installed
if(!"devtools" %in% installed.packages()){
    install.packages("devtools")
}

## install denovolyzeR
devtools::install_github("jamesware/denovolyzeR")

References and resources

The original description of the statistical framework implemented by denovolyzeR is published in Nature Genetics.
To cite denovolyzeR, please cite our manuscript in Current Protocols in Human Genetics, also available via PubMed Central. You can Click here to request a reprint of the manuscript.
The first study to apply denovolyzeR investigated the role of de novo variants in congenital heart disease, and has been published at Science. Click here to request a reprint of the manuscript if you do not have access.

Alternative mutational probability tables that can be downloaded for use with denovolyzeR can be found here.