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.
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 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