Deconvolute Mixed Genomes with Unknown Proportions

Traditional phasing programs are limited to diploid organisms. Our method modifies Li and Stephens algorithm with Markov chain Monte Carlo (MCMC) approaches, and builds a generic framework that allows haplotype searches in a multiple infection setting. This package is primarily developed as part of the Pf3k project, which is a global collaboration using the latest sequencing technologies to provide a high-resolution view of natural variation in the malaria parasite Plasmodium falciparum. Parasite DNA are extracted from patient blood sample, which often contains more than one parasite strain, with unknown proportions. This package is used for deconvoluting mixed haplotypes, and reporting the mixture proportions from each sample.


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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

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 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

News

Reference manual

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install.packages("DEploid")

0.5.0 by Joe Zhu, 3 days ago


https://github.com/mcveanlab/DEploid-r


Report a bug at https://github.com/mcveanlab/DEploid-r/issues


Browse source code at https://github.com/cran/DEploid


Authors: Joe Zhu [aut, cre, cph], Jacob Almagro-Garcia [aut, cph], Gil McVean [aut, cph], University of Oxford [cph], Yinghan Liu [ctb], CodeCogs Zyba Ltd [com, cph], Deepak Bandyopadhyay [com, cph], Lutz Kettner [com, cph]


Documentation:   PDF Manual  


GPL (>= 3) license


Imports Rcpp, scales, plotly, magrittr, rmarkdown, htmlwidgets

Suggests knitr, testthat

Linking to Rcpp

System requirements: C++11


See at CRAN