DEploid.utils-package {DEploid.utils}R Documentation

DEploid.utils: 'DEploid' Data Analysis and Results Interpretation

Description

'DEploid' (Zhu et.al. 2018 doi:10.1093/bioinformatics/btx530) 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 infection setting. This package provides R functions to support data analysis and results interpretation.

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.

Author(s)

Maintainer: Joe Zhu sha.joe.zhu@gmail.com (ORCID)

Authors:

Other contributors:

Joe Zhu

Maintainer: Joe Zhu sha.joe.zhu@gmail.com


[Package DEploid.utils version 0.0.1 Index]