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.

Documentation

Manual: DEploid.pdf
Vignette: dEploid-Arguments

Maintainer: Joe Zhu <joe.zhu at well.ox.ac.uk>

Author(s): Joe Zhu*

Install package and any missing dependencies by running this line in your R console:

install.packages("DEploid")

Depends R (>= 3.1.0)
Imports Rcpp(>=0.11.2)
Suggests knitr, rmarkdown, testthat(>=0.9.0)
Enhances
Linking to Rcpp
Reverse
depends
Reverse
imports
Reverse
suggests
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enhances
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linking to

Package DEploid
Materials
URL https://github.com/mcveanlab/DEploid-r
Task Views
Version 0.3.2
Published 2016-11-25
License GPL (>= 3)
BugReports https://github.com/mcveanlab/DEploid-r/issues
SystemRequirements C++11
NeedsCompilation yes
Citation
CRAN checks DEploid check results
Package source DEploid_0.3.2.tar.gz