scripts
Class DifferentialClusteringSolutionSignificanceEstimator

java.lang.Object
  scripts.DifferentialClusteringSolutionSignificanceEstimator

public class DifferentialClusteringSolutionSignificanceEstimator
extends java.lang.Object

This scripts evaluates the significance of the differential correlation within and between modules in a given solution. * The input contains: (1) expression matrix, (2) classes file, (3) the clustering solution file , and (4) a bit specifying if this is a solution of DICER or another algorithm. * 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. 4. 0 if the solution is not of DICER, 1 otherwise. This script evaluates the fold-change in DC between clusters as compared to random gene sets of the same size. Note, the output of this script was further analyzed for the paper to give preference only for "significant" module pairs of other algorithms.

Constructor Summary

DifferentialClusteringSolutionSignificanceEstimator()

Method Summary

static void	calculateDiffStatistics(TscoresCalculator sims, java.util.Hashtable<java.lang.String,java.util.HashSet<java.lang.String>> geneSets)
static void	calculateDiffStatistics(TscoresCalculator sims, java.util.LinkedList<java.util.LinkedList<java.lang.String>> geneSets)
static void	calculateDiffStatisticsForPairs(TscoresCalculator sims, java.util.Hashtable<java.lang.String,java.util.HashSet<java.lang.String>> geneSets) This method go over all set pairs and calculate the fold change against average of random modules.
static void	calculateDiffStatisticsForPairsForOurAlgo(TscoresCalculator sims, java.util.Hashtable<java.lang.String,java.util.HashSet<java.lang.String>> geneSets)
static java.util.ArrayList<java.lang.Integer>	getSetAsArrayList(TscoresCalculator sims, java.util.Collection<java.lang.String> geneSet)
static float	getSumOfScores(TscoresCalculator sims, java.util.Collection<java.lang.String> geneSet)
static float	getSumOfScores(TscoresCalculator sims, java.util.HashSet<java.lang.String> geneSet, java.util.HashSet<java.lang.String> geneSet2, boolean print)
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

DifferentialClusteringSolutionSignificanceEstimator

public DifferentialClusteringSolutionSignificanceEstimator()

Method Detail

main

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

Parameters:

args -

calculateDiffStatistics

public static void calculateDiffStatistics(TscoresCalculator sims,
                                           java.util.Hashtable<java.lang.String,java.util.HashSet<java.lang.String>> geneSets)

calculateDiffStatistics

public static void calculateDiffStatistics(TscoresCalculator sims,
                                           java.util.LinkedList<java.util.LinkedList<java.lang.String>> geneSets)

calculateDiffStatisticsForPairs

public static void calculateDiffStatisticsForPairs(TscoresCalculator sims,
                                                   java.util.Hashtable<java.lang.String,java.util.HashSet<java.lang.String>> geneSets)

This method go over all set pairs and calculate the fold change against average of random modules. The method returns a hash that contains the accepted pairs (max size = 20).

Parameters:

sims -

geneSets -

calculateDiffStatisticsForPairsForOurAlgo

public static void calculateDiffStatisticsForPairsForOurAlgo(TscoresCalculator sims,
                                                             java.util.Hashtable<java.lang.String,java.util.HashSet<java.lang.String>> geneSets)

getSumOfScores

public static float getSumOfScores(TscoresCalculator sims,
                                   java.util.Collection<java.lang.String> geneSet)

getSumOfScores

public static float getSumOfScores(TscoresCalculator sims,
                                   java.util.HashSet<java.lang.String> geneSet,
                                   java.util.HashSet<java.lang.String> geneSet2,
                                   boolean print)

getSetAsArrayList

public static java.util.ArrayList<java.lang.Integer> getSetAsArrayList(TscoresCalculator sims,
                                                                       java.util.Collection<java.lang.String> geneSet)