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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install.packages("ipADMIXTURE")

0.1.0 by Chainarong Amornbunchornvej, 7 months ago


https://github.com/DarkEyes/ipADMIXTURE


Report a bug at https://github.com/DarkEyes/ipADMIXTURE/issues


Browse source code at https://github.com/cran/ipADMIXTURE


Authors: Chainarong Amornbunchornvej [aut, cre]


Documentation:   PDF Manual  


GPL-3 license


Imports stats, treemap, ape

Suggests knitr, rmarkdown


See at CRAN