Package ubic.gemma.core.analysis.expression.coexpression.links

Class SpearmanMetrics

java.lang.Object

ubic.gemma.core.analysis.expression.coexpression.links.AbstractMatrixRowPairAnalysis

ubic.gemma.core.analysis.expression.coexpression.links.PearsonMetrics

ubic.gemma.core.analysis.expression.coexpression.links.SpearmanMetrics

All Implemented Interfaces:

MatrixRowPairAnalysis

public class SpearmanMetrics
extends PearsonMetrics

Subclass that computes correlations using ranks.

Author:

paul

Field Summary

Fields inherited from class ubic.gemma.core.analysis.expression.coexpression.links.AbstractMatrixRowPairAnalysis

HARD_LIMIT_MIN_NUM_USED

Fields inherited from interface ubic.gemma.core.analysis.expression.coexpression.links.MatrixRowPairAnalysis

NUM_BINS

Constructor Summary

Constructors

Modifier	Constructor	Description
protected	SpearmanMetrics(int size)
	SpearmanMetrics(ExpressionDataDoubleMatrix dataMatrix)
	SpearmanMetrics(ExpressionDataDoubleMatrix dataMatrix, double tmts)

Method Summary

Modifier and Type	Method	Description
void	calculateMetrics()	Compute correlations.
double	correctedPvalue(int i, int j, double correl, int numused)
QuantitationType	getMetricType()
protected void	rowStatistics()	Calculate mean and sumsqsqrt for each row -- using the ranks of course!
protected double	spearman(double[] vectorA, double[] vectorB, boolean[] usedA, boolean[] usedB, int i, int j)

Methods inherited from class ubic.gemma.core.analysis.expression.coexpression.links.PearsonMetrics

correlFast

Methods inherited from class ubic.gemma.core.analysis.expression.coexpression.links.AbstractMatrixRowPairAnalysis

getCrossHybridizationRejections, getHistogramArrayList, getKeepers, getMatrix, getNumUniqueGenes, getProbeForRow, getScoreInBin, isUsePvalueThreshold, kurtosis, nullMatrix, numCached, setDuplicateMap, setLowerTailThreshold, setMinNumpresent, setOmitNegativeCorrelationLinks, setPValueThreshold, setUpperTailThreshold, setUseAbsoluteValue, setUsePvalueThreshold, size, toString

Methods inherited from class java.lang.Object

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

Constructor Detail

SpearmanMetrics

public SpearmanMetrics(ExpressionDataDoubleMatrix dataMatrix)

SpearmanMetrics

public SpearmanMetrics(ExpressionDataDoubleMatrix dataMatrix,
                       double tmts)

Parameters:

dataMatrix - DenseDoubleMatrix2DNamed

tmts - Values of the correlation that are deemed too small to store in the matrix. Setting this as high as possible can greatly reduce memory requirements, but can slow things down.

SpearmanMetrics

protected SpearmanMetrics(int size)

Parameters:

size - Dimensions of the required (square) matrix.

Method Detail

calculateMetrics

public void calculateMetrics()

Compute correlations.

Specified by:

calculateMetrics in interface MatrixRowPairAnalysis

Overrides:

calculateMetrics in class PearsonMetrics

getMetricType

public QuantitationType getMetricType()

Specified by:

getMetricType in interface MatrixRowPairAnalysis

Overrides:

getMetricType in class PearsonMetrics

rowStatistics

protected void rowStatistics()

Calculate mean and sumsqsqrt for each row -- using the ranks of course!

Overrides:

rowStatistics in class PearsonMetrics

correctedPvalue

public double correctedPvalue(int i,
                              int j,
                              double correl,
                              int numused)

spearman

protected double spearman(double[] vectorA,
                          double[] vectorB,
                          boolean[] usedA,
                          boolean[] usedB,
                          int i,
                          int j)