scripts
Class HyperGeometricEnrichmentAnalysis

java.lang.Object
  scripts.HyperGeometricEnrichmentAnalysis

public class HyperGeometricEnrichmentAnalysis
extends java.lang.Object

Constructor Summary

HyperGeometricEnrichmentAnalysis(java.lang.String geneSetsFile, java.util.ArrayList<java.lang.String> bg, java.util.Hashtable<java.lang.String,java.util.HashSet<java.lang.String>> c)

Method Summary

void	calcResults()
void	calcResults(double p)
void	determineFDRThrIndependenceAssumption(double p)
java.util.HashSet<java.lang.String>	getEnrichedTerms()
static void	main(java.lang.String[] args)
void	printGenes()
void	printResults(double p)
void	printResultsStatistics(double p)
void	printResultsStatisticsRemoveDuplications(double p)
static java.util.Hashtable<java.lang.String,java.util.HashSet<java.lang.String>>	readGeneSets(java.lang.String path, java.util.Collection<java.lang.String> bg)
static java.util.Hashtable<java.lang.String,java.util.HashSet<java.lang.String>>	readGeneSets(java.lang.String path, java.util.HashSet<java.lang.String> bg)

Methods inherited from class java.lang.Object

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

Constructor Detail

HyperGeometricEnrichmentAnalysis

public HyperGeometricEnrichmentAnalysis(java.lang.String geneSetsFile,
                                        java.util.ArrayList<java.lang.String> bg,
                                        java.util.Hashtable<java.lang.String,java.util.HashSet<java.lang.String>> c)

Method Detail

calcResults

public void calcResults()

determineFDRThrIndependenceAssumption

public void determineFDRThrIndependenceAssumption(double p)

printResults

public void printResults(double p)

calcResults

public void calcResults(double p)

getEnrichedTerms

public java.util.HashSet<java.lang.String> getEnrichedTerms()

printResultsStatistics

public void printResultsStatistics(double p)

printResultsStatisticsRemoveDuplications

public void printResultsStatisticsRemoveDuplications(double p)

printGenes

public void printGenes()

main

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

readGeneSets

public static java.util.Hashtable<java.lang.String,java.util.HashSet<java.lang.String>> readGeneSets(java.lang.String path,
                                                                                                     java.util.HashSet<java.lang.String> bg)

readGeneSets

public static java.util.Hashtable<java.lang.String,java.util.HashSet<java.lang.String>> readGeneSets(java.lang.String path,
                                                                                                     java.util.Collection<java.lang.String> bg)