biclustFunc {ipADMIXTURE}

biclustFunc function

Description

biclustFunc is a binary clustering function using hierarchical clustering.

Usage

biclustFunc(Qmat, admixRatioThs = 0.5, 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 binary clustering results.

heteroFlag

is a flag that represents a status whether a given cluster is heterogeneous (having sub-clusters). It is TRUE if maxDiffAdmixRatio >= admixRatioThs.

clusterInx

is a vector of clustering assignment where indexClsVec[i] is a cluster number of individual i.

meanDiffAdmixRatio

is a vector of magnitude-difference of admixture ratios. It is calculated by splitting a given cluster into two sub-clusters. Then, we take the absolute on the difference between mean admixture ratios of sub-clusters.

Qmat1

is a Q matrix of sub-cluster #1 after splitting a given cluster into two sub-clusters that contains admixture ratios of all individuals where the Qmat[i,j] represents the admixture ratio of ancestor j for individual i.

Qmat2

is a Q matrix of sub-cluster #2 after splitting a given cluster into two sub-clusters that contains admixture ratios of all individuals where the Qmat[i,j] represents the admixture ratio of ancestor j for individual i.

maxDiffAdmixRatio

is a maximum of magnitude-difference of admixture ratios for a given cluster before splitting into two sub-clusters.

Examples

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