Class Hierarchical_Clustering

Object

Clustering

Hierarchical_Clustering

public class Hierarchical_Clustering
extends Clustering

An instance of the Hierarchical_Clustering class represents a clustering (i.e., grouping or partitioning) of a collection of genes using the centroid-linkage hierarchical clustering method.

Field Summary

Fields inherited from class Clustering

clusters, experiments, genes

Constructor Summary

Constructors

Constructor and Description
Hierarchical_Clustering(String fileName, int numClusters) Creates an initially empty Hierarchical_Clustering.

Method Summary

Modifier and Type	Method and Description
void	hierarchical() Performs centroid-linkage hierarchical clustering.
void	initiallyAssignOneGeneToEachCluster() Assigns each gene to its own unique cluster.
static void	main(String[] args) The main method creates a Clustering based on gene and experiment data from a tab-delimited text file.
void	mergeTwoClosestClusters() Identifies and merges together the two closest clusters.

Methods inherited from class Clustering

getExperimentNamesFromFile, getGeneInformationFromFile, getNumClusters, getNumExperiments, getNumGenes, toString

Methods inherited from class Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

Hierarchical_Clustering

public Hierarchical_Clustering(String fileName,
                               int numClusters)

Creates an initially empty Hierarchical_Clustering.

A set of genes and experiments are determined from the specified String representing the name of a file. Genes and experiments are read-in from the tab-delimited file. Initially, the constructed Hierarchical_Clustering is empty.

Parameters:

fileName - the name of a tab-delimited text file containing gene and experiment data

numClusters - an integer representing the desired number of clusters

Method Detail

initiallyAssignOneGeneToEachCluster

public void initiallyAssignOneGeneToEachCluster()

Assigns each gene to its own unique cluster.

Initially, each cluster contains only one gene. So the number of clusters is the same as the number of genes.

mergeTwoClosestClusters

public void mergeTwoClosestClusters()

Identifies and merges together the two closest clusters.

Identifies the two clusters that are closest together, i.e., whose mean expression vectors have the shortest distance between them. Then these two clusters are merged. In order to merge the two clusters, all genes in the second cluster are added to the first cluster and the second cluster is then removed. Thus, the total number of clusters is decreased by one following invocation of this method.

hierarchical

public void hierarchical()

Performs centroid-linkage hierarchical clustering.

Initially, each cluster contains one gene. The two closest clusters are identified (i.e., the two clusters whose mean expression vectors have the smallest distance between them), and these two clusters are merged into one cluster. The process is repeated, with each iteration reducing the number of clusters by one, until the desired number of final clusters is obtained.

main

public static void main(String[] args)

The main method creates a Clustering based on gene and experiment data from a tab-delimited text file.

The clustering is determined using centroid-linkage hierarchical clustering. The text file and the desired number of clusters are specified as command line arguments. The computed set of clusters is output to standard output (and can be redirected to a file).

Parameters:

args - an array of Strings representing any command line arguments