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

Class SVDServiceHelperImpl

java.lang.Object

ubic.gemma.core.analysis.preprocess.svd.SVDServiceHelperImpl

All Implemented Interfaces:

SVDServiceHelper

@Service
public class SVDServiceHelperImpl
extends Object
implements SVDServiceHelper

Perform SVD on expression data and store the results.

Author:

paul

See Also:

PrincipalComponentAnalysisService

Constructor Summary

Constructors

Constructor	Description
SVDServiceHelperImpl()

Method Summary

Modifier and Type	Method	Description
Set<ExperimentalFactor>	getImportantFactors(ExpressionExperiment ee, Collection<ExperimentalFactor> experimentalFactors, Double importanceThreshold)
Map<ProbeLoading,DoubleVectorValueObject>	getTopLoadedVectors(ExpressionExperiment ee, int component, int count)
boolean	hasPca(ExpressionExperiment ee)
static void	populateBMFMap(Map<ExperimentalFactor,Map<Long,Double>> bioMaterialFactorMap, BioMaterial bm)	Retrieve relationships between factors, biomaterials and factor values.
SVDValueObject	retrieveSvd(ExpressionExperiment ee)	Get the SVD information for experiment with id given.
SVDValueObject	svd(ExpressionExperiment ee)
SVDValueObject	svdFactorAnalysis(PrincipalComponentAnalysis pca)	Compare ExperimentalFactors and BioAssay.processingDates to the PCs.
SVDValueObject	svdFactorAnalysis(ExpressionExperiment ee)	Compare ExperimentalFactors and BioAssay.processingDates to the PCs.

Methods inherited from class java.lang.Object

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

Constructor Detail

SVDServiceHelperImpl

public SVDServiceHelperImpl()

Method Detail

populateBMFMap

public static void populateBMFMap(Map<ExperimentalFactor,Map<Long,Double>> bioMaterialFactorMap,
                                  BioMaterial bm)

Retrieve relationships between factors, biomaterials and factor values.

Continuous factor values are converted to a Double if possible, otherwise the FactorValue.getId() is used. This is the case for categorical measurement.

Parameters:

bioMaterialFactorMap - to be populated, of experimental factor -> biomaterial ID -> factor value (double value if possible otherwise ID)

bm - to populate for

retrieveSvd

@Transactional(readOnly=true)
public SVDValueObject retrieveSvd(ExpressionExperiment ee)

Get the SVD information for experiment with id given.

Specified by:

retrieveSvd in interface SVDServiceHelper

Returns:

value or null if there isn't one.

svd

@Transactional
public SVDValueObject svd(ExpressionExperiment ee)
                   throws SVDException

Specified by:

svd in interface SVDServiceHelper

Throws:

SVDException

getTopLoadedVectors

@Transactional(readOnly=true)
public Map<ProbeLoading,DoubleVectorValueObject> getTopLoadedVectors(ExpressionExperiment ee,
                                                                           int component,
                                                                           int count)

Specified by:

getTopLoadedVectors in interface SVDServiceHelper

hasPca

@Transactional(readOnly=true)
public boolean hasPca(ExpressionExperiment ee)

Specified by:

hasPca in interface SVDServiceHelper

getImportantFactors

@Transactional(readOnly=true)
public Set<ExperimentalFactor> getImportantFactors(ExpressionExperiment ee,
                                                   Collection<ExperimentalFactor> experimentalFactors,
                                                   Double importanceThreshold)

Specified by:

getImportantFactors in interface SVDServiceHelper

Parameters:

ee - the expression experiment

experimentalFactors - to consider

importanceThreshold - threshold for pvalue of association with factor. Suggested value might be 0.01.

Returns:

factors which are "significantly" associated with one of the first three PCs

svdFactorAnalysis

@Transactional(readOnly=true)
public SVDValueObject svdFactorAnalysis(PrincipalComponentAnalysis pca)

Description copied from interface: SVDServiceHelper

Compare ExperimentalFactors and BioAssay.processingDates to the PCs.

Specified by:

svdFactorAnalysis in interface SVDServiceHelper

Parameters:

pca - PCA

Returns:

SVD VO

svdFactorAnalysis

@Transactional(readOnly=true)
public SVDValueObject svdFactorAnalysis(ExpressionExperiment ee)

Description copied from interface: SVDServiceHelper

Compare ExperimentalFactors and BioAssay.processingDates to the PCs.

Specified by:

svdFactorAnalysis in interface SVDServiceHelper

Parameters:

ee - the experiment

Returns:

SVD VO