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An R interface for dEploid. dEploid is designed for deconvoluting 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 infe…

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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

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An R interface for dEploid. dEploid is designed for deconvoluting 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 infe…

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