ipADMIXTURE: Iterative Pruning Population Admixture Inference Framework...
In ipADMIXTURE: Iterative Pruning Population Admixture Inference Framework

Description Usage Arguments Value Author(s) Examples

View source: R/ipADMIXTURE.R

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.

1	ipADMIXTURE(Qmat, admixRatioThs, method = "average")

`Qmat`	is a Q matrix that contains admixture ratios of all individuals where the `Qmat[i,j]` represents the admixture ratio of ancestor j for individual i.
`admixRatioThs`	is a threshold to determine that if a cluster has `maxDiffAdmixRatio` lower than threshold, then the cluster is a homogeneous cluster.
`method`	is a method parameter of `hclust` object for hierarchical clustering analysis. The default is "average".

This function returns clustering results in a form of an object of ipADMIXTURE class. The object contains the following items.

`indexClsVec`	is a vector of clustering assignment where `indexClsVec[i]` is a cluster number of individual i.
`homoClusters`	is a list of cluster objects where each object contains member indices, cluster's `maxDiffAdmixRatio`, ID, etc.
`maxDiffAdmixRatioVec`	is a vector of `maxDiffAdmixRatio`s for all clusters.
`Qmat`	is a Q matrix that contains admixture ratios of all individuals where the `Qmat[i,j]` represents the admixture ratio of ancestor j for individual i.
`admixRatioThs`	is a threshold to determine that if a cluster has `maxDiffAdmixRatio` lower than threshold, then the cluster is a homogeneous cluster.

Chainarong Amornbunchornvej, chai@ieee.org

1 2	# Running ipADMIXTURE on Q matrix of 27 human population dataset where K = 12 h27pop_obj<-ipADMIXTURE(Qmat=ipADMIXTURE::human27pop_Qmat [[11]], admixRatioThs =0.15)