RhierBAPS: An R implementation of the population clustering algorithm hierBAPS.
Published version
Peer-reviewed
Repository URI
Repository DOI
Change log
Authors
Tonkin-Hill, Gerry https://orcid.org/0000-0003-4397-2224
Lees, John A https://orcid.org/0000-0001-5360-1254
Bentley, Stephen D
Frost, Simon DW
Corander, Jukka https://orcid.org/0000-0002-7752-1942
Abstract
Identifying structure in collections of sequence data sets remains a common problem in genomics. hierBAPS, a popular algorithm for identifying population structure in haploid genomes, has previously only been available as a MATLAB binary. We provide an R implementation which is both easier to install and use, automating the entire pipeline. Additionally, we allow for the use of multiple processors, improve on the default settings of the algorithm, and provide an interface with the ggtree library to enable informative illustration of the clustering results. Our aim is that this package aids in the understanding and dissemination of the method, as well as enhancing the reproducibility of population structure analyses.
Description
Keywords
R, clustering, population structure
Journal Title
Wellcome Open Res
Conference Name
Journal ISSN
2398-502X
2398-502X
2398-502X
Volume Title
3
Publisher
F1000 Research Ltd
Publisher DOI
Sponsorship
Wellcome Trust (204016/Z/16/Z)