org.geworkbench.util.associationdiscovery.statistics
Class ClusterStatistics

java.lang.Object
  org.geworkbench.util.associationdiscovery.statistics.ClusterStatistics

public class ClusterStatistics
extends java.lang.Object

Title: Plug And Play

Description: Dynamic Proxy Implementation of enGenious

Copyright: Copyright (c) 2002

Company: First Genetic Trust Inc.

Version:

1.0

Author:

Manjunath Kustagi

Field Summary

static int	binNo
static double	binSize
static java.util.HashMap	clusterStatistics
static double	DELTA
static double	DFLT_AXIS_RATIO
static double	DFLT_BOT_RATIO
static boolean	DFLT_SHOW_PDF
static boolean	DFLT_SHOWARGS
static boolean	DFLT_SHOWRESULT
static double	DFLT_TOP_RATIO
static double	EPSILON
static double	FPMIN
static int	ITMAX Variables needed for the statistical functions
static double	LANCZ_CUTOFF
static double	MAX_BOT_RATIO
static int	MAXPOINTS
static double[]	psi
static int	STEPS
static int	TICK_HEIGHT

Constructor Summary

ClusterStatistics(DSMicroarraySet mArraySet)

Method Summary

void	addCount(int geneId, double value, double p, double w)
double	avgPatternNo(int j, int k, int nj, int nk, double p)
double	betaCF(double a, double b, double x)
double	betaI(double a, double b, double x)
double	entropyRatio(CSMatchedMatrixPattern pattern)
static double	factLN(double n)
static double	gammaLN(double p)
static ClusterStatistics	getClusterStatistics(DSMicroarraySet microarraySet)
double	getExpectedNo(CSMatchedMatrixPattern pattern)
static double	getExpectedNo(DSMicroarraySet microarraySet, CSMatchedMatrixPattern pattern)
double	getExpectedNo(int j, int k)
double[]	getH(int k)
double	getP_Actual(CSMatchedMatrixPattern pattern)
double	getP_IID(CSMatchedMatrixPattern pattern)
void	histogram(double p)
void	init()
static double	logBinomialCoeff(int n, int k)
static double	logBinomialDistribution(int nj, int j, double p)
double	logMaximalP(int nm, int j, int k, double p)
double	maxEntropy(CSMatchedMatrixPattern pattern)
double	patternPValue(int j, int k, int nj, int nk, int j0, double p)
void	printHistogram()
void	reset()
void	resetHistogram()
static double	scorePattern(DSMicroarraySet<DSMicroarray> mArraySet, CSMatchedMatrixPattern pattern)
void	tabulateQjk()

Methods inherited from class java.lang.Object

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

Field Detail

ITMAX

public static final int ITMAX

Variables needed for the statistical functions

See Also:

Constant Field Values

FPMIN

public static final double FPMIN

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Constant Field Values

EPSILON

public static final double EPSILON

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Constant Field Values

DELTA

public static final double DELTA

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Constant Field Values

LANCZ_CUTOFF

public static final double LANCZ_CUTOFF

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Constant Field Values

MAXPOINTS

public static final int MAXPOINTS

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Constant Field Values

DFLT_AXIS_RATIO

public static final double DFLT_AXIS_RATIO

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Constant Field Values

DFLT_TOP_RATIO

public static final double DFLT_TOP_RATIO

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Constant Field Values

DFLT_BOT_RATIO

public static final double DFLT_BOT_RATIO

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Constant Field Values

MAX_BOT_RATIO

public static final double MAX_BOT_RATIO

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Constant Field Values

DFLT_SHOWARGS

public static final boolean DFLT_SHOWARGS

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Constant Field Values

DFLT_SHOWRESULT

public static final boolean DFLT_SHOWRESULT

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Constant Field Values

DFLT_SHOW_PDF

public static final boolean DFLT_SHOW_PDF

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Constant Field Values

TICK_HEIGHT

public static final int TICK_HEIGHT

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Constant Field Values

clusterStatistics

public static java.util.HashMap clusterStatistics

binNo

public static final int binNo

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Constant Field Values

binSize

public static final double binSize

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Constant Field Values

STEPS

public static final int STEPS

See Also:

Constant Field Values

psi

public static double[] psi

Constructor Detail

ClusterStatistics

public ClusterStatistics(DSMicroarraySet mArraySet)

Method Detail

betaCF

public double betaCF(double a,
                     double b,
                     double x)

betaI

public double betaI(double a,
                    double b,
                    double x)

gammaLN

public static double gammaLN(double p)

logMaximalP

public double logMaximalP(int nm,
                          int j,
                          int k,
                          double p)

logBinomialDistribution

public static double logBinomialDistribution(int nj,
                                             int j,
                                             double p)

factLN

public static double factLN(double n)

patternPValue

public double patternPValue(int j,
                            int k,
                            int nj,
                            int nk,
                            int j0,
                            double p)

logBinomialCoeff

public static double logBinomialCoeff(int n,
                                      int k)

avgPatternNo

public double avgPatternNo(int j,
                           int k,
                           int nj,
                           int nk,
                           double p)

reset

public void reset()

init

public void init()

addCount

public void addCount(int geneId,
                     double value,
                     double p,
                     double w)

tabulateQjk

public void tabulateQjk()

getExpectedNo

public double getExpectedNo(CSMatchedMatrixPattern pattern)

getExpectedNo

public double getExpectedNo(int j,
                            int k)

scorePattern

public static double scorePattern(DSMicroarraySet<DSMicroarray> mArraySet,
                                  CSMatchedMatrixPattern pattern)

getExpectedNo

public static double getExpectedNo(DSMicroarraySet microarraySet,
                                   CSMatchedMatrixPattern pattern)

getClusterStatistics

public static ClusterStatistics getClusterStatistics(DSMicroarraySet microarraySet)

getH

public double[] getH(int k)

resetHistogram

public void resetHistogram()

histogram

public void histogram(double p)

printHistogram

public void printHistogram()

maxEntropy

public double maxEntropy(CSMatchedMatrixPattern pattern)

getP_IID

public double getP_IID(CSMatchedMatrixPattern pattern)

getP_Actual

public double getP_Actual(CSMatchedMatrixPattern pattern)

entropyRatio

public double entropyRatio(CSMatchedMatrixPattern pattern)