Package ubic.gemma.model.analysis.expression.pca

Class PrincipalComponentAnalysis

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.pca.PrincipalComponentAnalysis

All Implemented Interfaces:

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

public class PrincipalComponentAnalysis
extends SingleExperimentAnalysis

See Also:

Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	PrincipalComponentAnalysis.Factory

Constructor Summary

Constructors

Constructor	Description
PrincipalComponentAnalysis()

Method Summary

Modifier and Type	Method	Description
BioAssayDimension	getBioAssayDimension()
Set<Eigenvalue>	getEigenValues()
List<Double[]>	getEigenvectorArrays()
Set<Eigenvector>	getEigenVectors()
Integer	getMaxNumProbesPerComponent()
Integer	getNumComponentsStored()
Set<ProbeLoading>	getProbeLoadings()
double[]	getVarianceFractions()
void	setBioAssayDimension(BioAssayDimension bioAssayDimension)
void	setEigenValues(Set<Eigenvalue> eigenValues)
void	setEigenVectors(Set<Eigenvector> eigenVectors)
void	setMaxNumProbesPerComponent(Integer maxNumProbesPerComponent)
void	setNumComponentsStored(Integer numComponentsStored)
void	setProbeLoadings(Set<ProbeLoading> probeLoadings)

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 gemma.gsec.model.Securable

getId

Constructor Detail

PrincipalComponentAnalysis

public PrincipalComponentAnalysis()

Method Detail

getBioAssayDimension

public BioAssayDimension getBioAssayDimension()

setBioAssayDimension

public void setBioAssayDimension(BioAssayDimension bioAssayDimension)

getEigenValues

public Set<Eigenvalue> getEigenValues()

setEigenValues

public void setEigenValues(Set<Eigenvalue> eigenValues)

getEigenVectors

public Set<Eigenvector> getEigenVectors()

setEigenVectors

public void setEigenVectors(Set<Eigenvector> eigenVectors)

getMaxNumProbesPerComponent

public Integer getMaxNumProbesPerComponent()

Returns:

How many probe loadings were stored per component (max).

setMaxNumProbesPerComponent

public void setMaxNumProbesPerComponent(Integer maxNumProbesPerComponent)

getNumComponentsStored

public Integer getNumComponentsStored()

Returns:

How many components results are stored for (e.g. 3)

setNumComponentsStored

public void setNumComponentsStored(Integer numComponentsStored)

getProbeLoadings

public Set<ProbeLoading> getProbeLoadings()

setProbeLoadings

public void setProbeLoadings(Set<ProbeLoading> probeLoadings)

getEigenvectorArrays

public List<Double[]> getEigenvectorArrays()
                                    throws IllegalArgumentException

Returns:

Convenience method to access the eigenvectors, as a List of Double[].

Throws:

IllegalArgumentException

getVarianceFractions

public double[] getVarianceFractions()

Returns:

An array of values representing the fraction of the variance each component accounts for. Convenience method to access the Eigenvalue data.