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

Class SVDServiceImpl

java.lang.Object

ubic.gemma.core.analysis.preprocess.svd.SVDServiceImpl

All Implemented Interfaces:

SVDService

@Service
public class SVDServiceImpl
extends Object
implements SVDService

Perform SVD on expression data and store the results.

Author:

paul

See Also:

• PrincipalComponentAnalysisService

Constructor Summary

Constructors

Constructor	Description
SVDServiceImpl()

Method Summary

Modifier and Type	Method	Description
Set<ExperimentalFactor>	getImportantFactors(ExpressionExperiment ee, Collection<ExperimentalFactor> experimentalFactors, Double importanceThreshold)
SVDResult	getSvd(ExpressionExperiment ee)	Get the SVD information for experiment with id given.
SVDResult	getSvdFactorAnalysis(PrincipalComponentAnalysis pca)	Compare ExperimentalFactors and BioAssay.processingDates to the PCs.
SVDResult	getSvdFactorAnalysis(ExpressionExperiment ee)	Compare ExperimentalFactors and BioAssay.processingDates to the PCs.
Map<ProbeLoading,DoubleVectorValueObject>	getTopLoadedVectors(ExpressionExperiment ee, int component, int count)
boolean	hasSvd(ExpressionExperiment ee)	Check if a dataset has a SVD analysis.
static void	populateBMFMap(Map<ExperimentalFactor,Map<BioMaterial,Number>> bioMaterialFactorMap, BioMaterial bm)	Retrieve relationships between factors, biomaterials and factor values.
SVDResult	svd(ExpressionExperiment ee)	Compute and update the SVD analysis fo the given experiment.

Methods inherited from class java.lang.Object

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

Constructor Details

SVDServiceImpl

public SVDServiceImpl()

Method Details

populateBMFMap

public static void populateBMFMap(Map<ExperimentalFactor,Map<BioMaterial,Number>> 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

getSvd

@Transactional(readOnly=true)
public SVDResult getSvd(ExpressionExperiment ee)

Get the SVD information for experiment with id given.

Specified by:

getSvd in interface SVDService

Returns:

value or null if there isn't one.

svd

@Transactional
public SVDResult svd(ExpressionExperiment ee)
              throws SVDException

Description copied from interface: SVDService

Compute and update the SVD analysis fo the given experiment.

Specified by:

svd in interface SVDService

Throws:

SVDException

getTopLoadedVectors

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

Specified by:

getTopLoadedVectors in interface SVDService

hasSvd

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

Description copied from interface: SVDService

Check if a dataset has a SVD analysis.

Specified by:

hasSvd in interface SVDService

getImportantFactors

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

Specified by:

getImportantFactors in interface SVDService

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

getSvdFactorAnalysis

@Transactional(readOnly=true)
public SVDResult getSvdFactorAnalysis(ExpressionExperiment ee)

Description copied from interface: SVDService

Compare ExperimentalFactors and BioAssay.processingDates to the PCs.

Specified by:

getSvdFactorAnalysis in interface SVDService

Parameters:

ee - the experiment

Returns:

SVD VO

getSvdFactorAnalysis

@Transactional(readOnly=true)
public SVDResult getSvdFactorAnalysis(PrincipalComponentAnalysis pca)

Description copied from interface: SVDService

Compare ExperimentalFactors and BioAssay.processingDates to the PCs.

Specified by:

getSvdFactorAnalysis in interface SVDService

Parameters:

pca - PCA

Returns:

SVD VO