scripts
Class DifferentialCorrelationOfClusteringAnalyzer

java.lang.Object
  scripts.DifferentialCorrelationOfClusteringAnalyzer

public class DifferentialCorrelationOfClusteringAnalyzer
extends java.lang.Object

This script is for evaluating a clustering solution. The input contains: (1) expression matrix, (2) classes file, and (3) the clustering solution file. * 1. A gene expression matrix file. This is a tab delimited file in which the first row contains the condition names, and the first column contains the gene names. For example, see the LungCancer.txt file LungCancer.zip. 2. A "classes file". This file contains partitioning of the conditions in the matrix to groups. We assume that conditions from the same groups are adjacent in the matrix. This file is tab delimited, in each row there are three columns: the start index of the current group (enumeration of the conditions starts from zero),the end index, and the group name. For example, see the classesFile.txt in LungCancer.zip 3. This is a tab-delimited file. Each line is of the format gene_name \t cluster_name. Given a clustering solution (gene tab cluster) it calculates: 1. Differential correlation statistics of the clusters: Average absolute DC Average weighted (by cluster size) absolute DC Average cluster size The number of the clusters in the solution 2. Enrichment analysis results of the clusters (FDR 0.05). To run this script two files should be in the running directory: humanGenes2KeggNames.txt Entrez2ProteinComplexes.txt These files contain mapping of genes to functional terms (pathways or protein complexes). Their format is the same as that of a clustering solution (gene tab term). If these files are not in the running directory, an exception will appear. In this case the output will contain the DC analysis results and the exception. Other remarks: A gene set named "grey" will be excluded from this analysis. This cluster name may appear in DiffCoEx solution. The genes in this "cluster" are genes that are to be excluded from DiffCoEx solution. Unlike DifferentialClusteringSolutionSignificanceEstimator this script is for analyzing the DC within clusters, without a comparison to random gene sets.

Constructor Summary

DifferentialCorrelationOfClusteringAnalyzer()

Method Summary

static void

main(java.lang.String[] args)

Methods inherited from class java.lang.Object

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

Constructor Detail

DifferentialCorrelationOfClusteringAnalyzer

public DifferentialCorrelationOfClusteringAnalyzer()

Method Detail

main

public static void main(java.lang.String[] args)

Parameters:

args -