Package ubic.gemma.core.analysis.preprocess.svd

Class SVDValueObject

java.lang.Object

ubic.gemma.core.analysis.preprocess.svd.SVDValueObject

All Implemented Interfaces:

Serializable

public class SVDValueObject
extends Object
implements Serializable

Store information about SVD of expression data and comparisons to factors/batch information.

Author:

paul

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor	Description
SVDValueObject()
SVDValueObject(Long id, List<Long> bioMaterialIds, double[] variances, DoubleMatrix<Long,Integer> vMatrix)
SVDValueObject(PrincipalComponentAnalysis pca)

Method Summary

Modifier and Type	Method	Description
Long[]	getBioMaterialIds()
Map<Integer,Double>	getDateCorrelations()
Map<Integer,Double>	getDatePvals()
List<Date>	getDates()
Map<Integer,Map<Long,Double>>	getFactorCorrelations()
Map<Integer,Map<Long,Double>>	getFactorPvals()
Map<Long,List<Double>>	getFactors()
Long	getId()
double[]	getVariances()
DoubleMatrix<Long,Integer>	getvMatrix()
void	setBioMaterialIds(Long[] bioMaterialIds)
void	setDateCorrelations(Map<Integer,Double> dateCorrelations)
void	setFactorCorrelations(Map<Integer,Map<Long,Double>> factorCorrelations)
void	setId(Long id)
void	setPCDateCorrelation(int componentNumber, double dateCorrelation)
void	setPCDateCorrelationPval(int componentNumber, double spearmanPvalue)
void	setPCFactorCorrelation(int componentNumber, ExperimentalFactor ef, double factorCorrelation)
void	setPCFactorCorrelationPval(int componentNumber, ExperimentalFactor ef, double pvalue)
void	setVariances(double[] variances)
void	setvMatrix(DoubleMatrix<Long,Integer> vMatrix)

Methods inherited from class java.lang.Object

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

Constructor Detail

SVDValueObject

public SVDValueObject()

SVDValueObject

public SVDValueObject(Long id,
                      List<Long> bioMaterialIds,
                      double[] variances,
                      DoubleMatrix<Long,Integer> vMatrix)

SVDValueObject

public SVDValueObject(PrincipalComponentAnalysis pca)

Method Detail

getBioMaterialIds

public Long[] getBioMaterialIds()

setBioMaterialIds

public void setBioMaterialIds(Long[] bioMaterialIds)

getDateCorrelations

public Map<Integer,Double> getDateCorrelations()

Returns:

Map of component to correlation that component with "batch/scan date" (the dates associated with BioAssays)

setDateCorrelations

public void setDateCorrelations(Map<Integer,Double> dateCorrelations)

getDatePvals

public Map<Integer,Double> getDatePvals()

getDates

public List<Date> getDates()

getFactorCorrelations

public Map<Integer,Map<Long,Double>> getFactorCorrelations()

Returns:

map of component to a map of ExperimentalFactor IDs to correlations of that factor with the component.

setFactorCorrelations

public void setFactorCorrelations(Map<Integer,Map<Long,Double>> factorCorrelations)

getFactorPvals

public Map<Integer,Map<Long,Double>> getFactorPvals()

Returns:

map of component to map of ExperimentalFactor IDs to pvalues for the association of that factor with the component.

getFactors

public Map<Long,List<Double>> getFactors()

getId

public Long getId()

setId

public void setId(Long id)

getVariances

public double[] getVariances()

Returns:

An array of values representing the fraction of the variance each component accounts for

setVariances

public void setVariances(double[] variances)

getvMatrix

public DoubleMatrix<Long,Integer> getvMatrix()

Returns:

Row names: biomaterial ids; column names: eigengene number (from 0)

setvMatrix

public void setvMatrix(DoubleMatrix<Long,Integer> vMatrix)

setPCDateCorrelation

public void setPCDateCorrelation(int componentNumber,
                                 double dateCorrelation)

setPCDateCorrelationPval

public void setPCDateCorrelationPval(int componentNumber,
                                     double spearmanPvalue)

setPCFactorCorrelation

public void setPCFactorCorrelation(int componentNumber,
                                   ExperimentalFactor ef,
                                   double factorCorrelation)

setPCFactorCorrelationPval

public void setPCFactorCorrelationPval(int componentNumber,
                                       ExperimentalFactor ef,
                                       double pvalue)