Package ubic.gemma.model.analysis.expression.coexpression

Class SampleCoexpressionAnalysis

java.lang.Object

ubic.gemma.model.common.AbstractDescribable

ubic.gemma.model.analysis.Analysis

ubic.gemma.model.analysis.expression.ExpressionAnalysis

ubic.gemma.model.analysis.SingleExperimentAnalysis

ubic.gemma.model.analysis.expression.coexpression.SampleCoexpressionAnalysis

All Implemented Interfaces:

gemma.gsec.model.Securable, gemma.gsec.model.SecuredChild, Serializable, Securable, SecuredChild, Describable, Identifiable

public class SampleCoexpressionAnalysis
extends SingleExperimentAnalysis

The 'analysis' in the name is a bit of a stretch here, as this object servers purely as an aggregator of all the sample coexpression matrices.

See Also:

Serialized Form

Constructor Summary

Constructors

Modifier	Constructor	Description
protected	SampleCoexpressionAnalysis()
	SampleCoexpressionAnalysis(BioAssaySet experimentAnalyzed, SampleCoexpressionMatrix fullCoexpressionMatrix, SampleCoexpressionMatrix regressedCoexpressionMatrix)

Method Summary

Modifier and Type	Method	Description
SampleCoexpressionMatrix	getBestCoexpressionMatrix()
SampleCoexpressionMatrix	getFullCoexpressionMatrix()	Note that since you get a full square matrix, all correlations are represented twice, and values on the main diagonal will always be 1.
SampleCoexpressionMatrix	getRegressedCoexpressionMatrix()	Note that since you get a full square matrix, all correlations are represented twice, and values on the main diagonal will always be 1.
void	setFullCoexpressionMatrix(SampleCoexpressionMatrix rawFullCoexpressionMatrix)
void	setRegressedCoexpressionMatrix(SampleCoexpressionMatrix regressedCoexpressionMatrix)

Methods inherited from class ubic.gemma.model.analysis.SingleExperimentAnalysis

getExperimentAnalyzed, getNumberOfElementsAnalyzed, getSecurityOwner, setExperimentAnalyzed, setNumberOfElementsAnalyzed

Methods inherited from class ubic.gemma.model.analysis.Analysis

getProtocol, setProtocol

Methods inherited from class ubic.gemma.model.common.AbstractDescribable

equals, getDescription, getId, getName, hashCode, setDescription, setId, setName, toString

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface ubic.gemma.model.common.Identifiable

getId

Methods inherited from interface gemma.gsec.model.Securable

getId

Constructor Detail

SampleCoexpressionAnalysis

protected SampleCoexpressionAnalysis()

SampleCoexpressionAnalysis

public SampleCoexpressionAnalysis(BioAssaySet experimentAnalyzed,
                                  SampleCoexpressionMatrix fullCoexpressionMatrix,
                                  @Nullable
                                  SampleCoexpressionMatrix regressedCoexpressionMatrix)

Method Detail

getFullCoexpressionMatrix

public SampleCoexpressionMatrix getFullCoexpressionMatrix()

Note that since you get a full square matrix, all correlations are represented twice, and values on the main diagonal will always be 1.

Returns:

a coexpression matrix with all factors (none regressed out), and including outliers.

setFullCoexpressionMatrix

public void setFullCoexpressionMatrix(SampleCoexpressionMatrix rawFullCoexpressionMatrix)

getRegressedCoexpressionMatrix

@Nullable
public SampleCoexpressionMatrix getRegressedCoexpressionMatrix()

Note that since you get a full square matrix, all correlations are represented twice, and values on the main diagonal will always be 1.

Returns:

a coexpression matrix with regressed out major factors.

setRegressedCoexpressionMatrix

public void setRegressedCoexpressionMatrix(@Nullable
                                           SampleCoexpressionMatrix regressedCoexpressionMatrix)

getBestCoexpressionMatrix

public SampleCoexpressionMatrix getBestCoexpressionMatrix()