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DEploid R package – Deconvolute Mixed Genomes with Unknown Proportions

Traditional ‘phasing’ programs are limited to diploid organisms. Our method modifies Li and Stephen’s algorithm with Markov chain Monte Carlo (MCMC) approaches, and builds a generic framework that allows haloptype searches in a multiple infection setting.

Installation

It is recommended to use the current CRAN version. It can be installed from within R using

> install.packages('DEploid')

For the developing version, please install Rcpp package first. From the R-console, type

> install.packages("Rcpp")

(NOTE: If you are using Windows, please install Rtools from https://cran.r-project.org/bin/windows/Rtools/)

then

> install.packages("devtools")
> library(devtools)
> install_github("mcveanlab/DEploid-r")

Usage

Please refer to the help page and examples for each function. For example,

> library(DEploid)
> ?dEploid
> ?plotProportions

Licence

You can freely use all code in this project under the conditions of the GNU GPL Version 3 or later.

Citation

If you use dEploid with the flag -ibd, please cite the following paper:

Zhu, J. S., J. A. Hendry, J. Almagro-Garcia, R. D. Pearson, R. Amato, A. Miles, D. J. Weiss, T. C. D. Lucas, M. Nguyen, P. W. Gething, D. Kwiatkowski, G. McVean, and for the Pf3k Project. (2018) The origins and relatedness structure of mixed infections vary with local prevalence of P. falciparum malaria. biorxiv, doi: https://doi.org/10.1101/387266.

If you use dEploid in your work, please cite the program:

Zhu, J. S. J. A. Garcia G. McVean. (2017) Deconvoluting multiple infections in Plasmodium falciparum from high throughput sequencing data. bioRxiv 099499. doi: https://doi.org/10.1101/099499