ipADMIXTURE {ipADMIXTURE}

Iterative Pruning Population Admixture Inference Framework (ipADMIXTURE)

Description

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.

Usage

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

Arguments

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".

Value

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 maxDiffAdmixRatios 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.

Author(s)

Chainarong Amornbunchornvej, [e-mail]

Examples

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