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.
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
(NOTE: If you are using Windows, please install
Rtools from https://cran.r-project.org/bin/windows/Rtools/)
> install.packages("devtools") > library(devtools) > install_github("mcveanlab/DEploid-r")
Please refer to the help page and examples for each function. For example,
> library(DEploid) > ?dEploid > ?plotProportions
You can freely use all code in this project under the conditions of the GNU GPL Version 3 or later.
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