Iterative Pruning Population Admixture Inference Framework

A data clustering package based on admixture ratios (Q matrix) of population structure. The framework is based on iterative Pruning procedure that performs data clustering by splitting a given population into subclusters until meeting the condition of stopping criteria the same as ipPCA, iNJclust, and IPCAPS frameworks. The package also provides a function to retrieve phylogeny tree that construct a neighbor-joining tree based on a similar matrix between clusters. By given multiple Q matrices with varying a number of ancestors (K), the framework define a similar value between clusters i,j as a minimum number K* that makes majority of members of two clusters are in the different clusters. This K* reflexes a minimum number of ancestors we need to splitting cluster i,j into different clusters if we assign K* clusters based on maximum admixture ratio of individuals. The publication of this package is at Chainarong Amornbunchornvej, Pongsakorn Wangkumhang, and Sissades Tongsima (2020) .


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0.1.0 by Chainarong Amornbunchornvej, 2 years ago

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Authors: Chainarong Amornbunchornvej [aut, cre]

Documentation:   PDF Manual  

GPL-3 license

Imports stats, treemap, ape

Suggests knitr, rmarkdown

See at CRAN