Poppr: an R package for genetic analysis of populations with clonal or partially clonal reproduction
A peer-reviewed article of this Preprint also exists.
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Abstract
Many microbial, fungal, or oomcyete populations violate assumptions for population genetic analysis because these populations are clonal or partially clonal. Furthermore, few tools exist that are specifically designed for analyzing data from clonal populations, making analysis difficult and haphazard. We developed the R package poppr providing unique tools for analysis of data from admixed, clonal, and/or mixed populations. Currently, poppr can be used for dominant/codominant and haploid/diploid genetic data. Data can be imported from several formats including GenAlEx formatted text files and can be analyzed on a user-defined hierarchy that includes unlimited levels of subpopulation structure and clone censoring. New functions include calculation of Bruvo’s distance for microsatellites, batch-analysis of the index of association with several indices of genotypic diversity, and graphing including dendrograms with bootstrap support and minimum spanning networks. A manual with documentation and examples is provided. Poppr is open source and major releases are available on CRAN: http://cran.r-project.org/package=poppr. More supporting documentation and tutorials can be found under ‘resources’ at: http://grunwaldlab.cgrb.oregonstate.edu/.
Cite this as
2013. Poppr: an R package for genetic analysis of populations with clonal or partially clonal reproduction. PeerJ PrePrints 1:e161v1 https://doi.org/10.7287/peerj.preprints.161v1note This preprint is not peer-reviewed. You may wish to reference the subsequent peer-reviewed version of this article.
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Competing Interests
NJG is an Academic Editor for PeerJ. The authors declare no additional competing interests.
Author Contributions
Zhian N Kamvar conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper.
Javier F Tabima conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools.
Niklaus J Grünwald conceived and designed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper.
Grant Disclosures
The following grant information was disclosed by the authors:
USDA NIFA grant: 2011-68004-30154
Data Deposition
The following information was supplied regarding the deposition of related data:
https://github.com/grunwaldlab/poppr
http://cran.r-project.org/package=poppr
Funding
The work was funded in part by USDA ARS and USDA NIFA. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
