Class ExpressionDataMatrixServiceImpl

java.lang.Object

ubic.gemma.core.analysis.service.ExpressionDataMatrixServiceImpl

All Implemented Interfaces:

ExpressionDataMatrixService

@Component
public class ExpressionDataMatrixServiceImpl
extends Object
implements ExpressionDataMatrixService

Tools for easily getting data matrices for analysis in a consistent way.

Author:

keshav

Constructor Summary

Constructors

Constructor	Description
ExpressionDataMatrixServiceImpl()

Method Summary

Modifier and Type	Method	Description
ExpressionDataDoubleMatrix	getFilteredMatrix(Collection<ProcessedExpressionDataVector> dataVectors, ArrayDesign arrayDesign, ExpressionExperimentFilterConfig filterConfig, boolean logTransform)
ExpressionDataDoubleMatrix	getFilteredMatrix(ExpressionExperiment ee, Collection<ProcessedExpressionDataVector> dataVectors, ExpressionExperimentFilterConfig filterConfig, boolean logTransform)	Provide a filtered expression data matrix.
ExpressionDataDoubleMatrix	getFilteredMatrix(ExpressionExperiment ee, Collection<ProcessedExpressionDataVector> dataVectors, ExpressionExperimentFilterConfig filterConfig, boolean logTransform, ExpressionExperimentFilterResult result)	Provide a filtered expression data matrix, reporting the per-stage attrition into a caller-supplied result.
ExpressionDataDoubleMatrix	getFilteredMatrix(ExpressionExperiment ee, ExpressionExperimentFilterConfig filterConfig)	Provide a filtered expression data matrix.
ExpressionDataDoubleMatrix	getProcessedExpressionDataMatrix(ExpressionExperiment ee)	Obtain the processed expression data matrix for a given experiment.
ExpressionDataDoubleMatrix	getProcessedExpressionDataMatrix(ExpressionExperiment ee, boolean thawAssays)
ExpressionDataDoubleMatrix	getProcessedExpressionDataMatrix(ExpressionExperiment ee, List<BioAssay> samples)
DoubleMatrix<Gene, ExpressionExperiment>	getRankMatrix(Collection<Gene> genes, Collection<ExpressionExperiment> ees, ProcessedExpressionDataVectorDao.RankMethod method)
ExpressionDataDoubleMatrix	getRawExpressionDataMatrix(ExpressionExperiment ee, List<BioAssay> samples, QuantitationType quantitationType)
ExpressionDataDoubleMatrix	getRawExpressionDataMatrix(ExpressionExperiment ee, QuantitationType quantitationType)	Obtain a raw expression data matrix for a given quantitation type

Methods inherited from class Object

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

Constructor Details

ExpressionDataMatrixServiceImpl

public ExpressionDataMatrixServiceImpl()

Method Details

getFilteredMatrix

@Transactional(readOnly=true)
public ExpressionDataDoubleMatrix getFilteredMatrix(ExpressionExperiment ee,
 ExpressionExperimentFilterConfig filterConfig)
                                             throws FilteringException

Description copied from interface: ExpressionDataMatrixService

Provide a filtered expression data matrix.

Specified by:

getFilteredMatrix in interface ExpressionDataMatrixService

Parameters:

ee - the expression experiment.

filterConfig - the configuration.

Returns:

data matrix

Throws:

FilteringException

getFilteredMatrix

@Transactional(readOnly=true)
public ExpressionDataDoubleMatrix getFilteredMatrix(ExpressionExperiment ee,
 Collection<ProcessedExpressionDataVector> dataVectors,
 ExpressionExperimentFilterConfig filterConfig,
 boolean logTransform)
                                             throws FilteringException

Description copied from interface: ExpressionDataMatrixService

Provide a filtered expression data matrix.

Specified by:

getFilteredMatrix in interface ExpressionDataMatrixService

Parameters:

ee - the expression experiment.

dataVectors - data vectors

filterConfig - the configuration.

logTransform - perform a log transformation on the data, this is ignored if the data is already on a log scale, the default is to return the data as is.

Returns:

data matrix

Throws:

FilteringException

getFilteredMatrix

@Transactional(readOnly=true)
public ExpressionDataDoubleMatrix getFilteredMatrix(ExpressionExperiment ee,
 Collection<ProcessedExpressionDataVector> dataVectors,
 ExpressionExperimentFilterConfig filterConfig,
 boolean logTransform,
 ExpressionExperimentFilterResult result)
                                             throws FilteringException

Description copied from interface: ExpressionDataMatrixService

Provide a filtered expression data matrix, reporting the per-stage attrition into a caller-supplied result.

The other overloads discard that result. Use this one when the attrition is wanted as well as the matrix -- the sample-correlation run records it on the audit event so a curator can see how many design elements each filter removed.

Specified by:

getFilteredMatrix in interface ExpressionDataMatrixService

Parameters:

result - populated in place as each filter runs; untouched if filtering throws

Throws:

FilteringException

See Also:

• SampleCorrelationAnalysisPayload

getFilteredMatrix

@Transactional(readOnly=true)
public ExpressionDataDoubleMatrix getFilteredMatrix(Collection<ProcessedExpressionDataVector> dataVectors,
 ArrayDesign arrayDesign,
 ExpressionExperimentFilterConfig filterConfig,
 boolean logTransform)
                                             throws FilteringException

Specified by:

getFilteredMatrix in interface ExpressionDataMatrixService

Throws:

FilteringException

getProcessedExpressionDataMatrix

@Transactional(readOnly=true)
public ExpressionDataDoubleMatrix getProcessedExpressionDataMatrix(ExpressionExperiment ee)

Description copied from interface: ExpressionDataMatrixService

Obtain the processed expression data matrix for a given experiment.

Specified by:

getProcessedExpressionDataMatrix in interface ExpressionDataMatrixService

getProcessedExpressionDataMatrix

@Transactional(readOnly=true)
public ExpressionDataDoubleMatrix getProcessedExpressionDataMatrix(ExpressionExperiment ee,
 boolean thawAssays)

Specified by:

getProcessedExpressionDataMatrix in interface ExpressionDataMatrixService

Parameters:

ee - the expression experiment.

thawAssays - whether to thaw the assays or not using Thaws.thawBioAssayDimension(BioAssayDimension)

Returns:

matrix of preferred data, with all missing values masked

getProcessedExpressionDataMatrix

@Transactional(readOnly=true)
public ExpressionDataDoubleMatrix getProcessedExpressionDataMatrix(ExpressionExperiment ee,
 List<BioAssay> samples)

Specified by:

getProcessedExpressionDataMatrix in interface ExpressionDataMatrixService

getRawExpressionDataMatrix

@Transactional(readOnly=true)
public ExpressionDataDoubleMatrix getRawExpressionDataMatrix(ExpressionExperiment ee,
 QuantitationType quantitationType)

Description copied from interface: ExpressionDataMatrixService

Obtain a raw expression data matrix for a given quantitation type

Specified by:

getRawExpressionDataMatrix in interface ExpressionDataMatrixService

getRawExpressionDataMatrix

@Transactional(readOnly=true)
public ExpressionDataDoubleMatrix getRawExpressionDataMatrix(ExpressionExperiment ee,
 List<BioAssay> samples,
 QuantitationType quantitationType)

Specified by:

getRawExpressionDataMatrix in interface ExpressionDataMatrixService

getRankMatrix

@Transactional(readOnly=true)
public DoubleMatrix<Gene, ExpressionExperiment> getRankMatrix(Collection<Gene> genes,
 Collection<ExpressionExperiment> ees,
 ProcessedExpressionDataVectorDao.RankMethod method)

Specified by:

getRankMatrix in interface ExpressionDataMatrixService