ipADMIXTURE (0.1.0)

0 users

Iterative Pruning Population Admixture Inference Framework.

https://github.com/DarkEyes/ipADMIXTURE
http://cran.r-project.org/web/packages/ipADMIXTURE

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) .

Maintainer: Chainarong Amornbunchornvej
Author(s): Chainarong Amornbunchornvej [aut, cre] (<https://orcid.org/0000-0003-3131-0370>)

License: GPL-3

Uses: ape, treemap, knitr, rmarkdown

Released 11 days ago.


Ratings

Overall:

  (0 votes)

Documentation:

  (0 votes)

Log in to vote.

Reviews

No one has written a review of ipADMIXTURE yet. Want to be the first? Write one now.


Related packages:(20 best matches, based on common tags.)


Search for ipADMIXTURE on google, google scholar, r-help, r-devel.

Visit ipADMIXTURE on R Graphical Manual.