Package ubic.gemma.persistence.service.analysis.expression.sampleCoexpression

Interface SampleCoexpressionAnalysisService

All Known Implementing Classes:

SampleCoexpressionAnalysisServiceImpl

public interface SampleCoexpressionAnalysisService

Author:

Paul

Method Summary

Modifier and Type	Method	Description
DoubleMatrix<BioAssay,BioAssay>	compute(ExpressionExperiment ee, PreparedCoexMatrices matrices)	Computes sample correlation matrices for the given experiment.
boolean	hasAnalysis(ExpressionExperiment ee)
DoubleMatrix<BioAssay,BioAssay>	loadBestMatrix(ExpressionExperiment ee)	Loads the analysis containing the coexpression matrices for the given experiment and converts the regressed coexpression matrix into a double matrix.
DoubleMatrix<BioAssay,BioAssay>	loadFullMatrix(ExpressionExperiment ee)	Loads the analysis containing the coexpression matrices for the given experiment and converts the full (non-regressed) coexpression matrix into a double matrix.
DoubleMatrix<BioAssay,BioAssay>	loadRegressedMatrix(ExpressionExperiment ee)	Load the regressed coexpression matrix for the given experiment.
PreparedCoexMatrices	prepare(ExpressionExperiment ee)
void	removeForExperiment(ExpressionExperiment ee)	Removes all coexpression matrices for the given experiment.
DoubleMatrix<BioAssay,BioAssay>	retrieveExisting(ExpressionExperiment ee)

Method Detail

loadFullMatrix

@Nullable
DoubleMatrix<BioAssay,BioAssay> loadFullMatrix(ExpressionExperiment ee)

Loads the analysis containing the coexpression matrices for the given experiment and converts the full (non-regressed) coexpression matrix into a double matrix. If the analysis or the matrix does not exist, computes it.

Parameters:

ee - the experiment to load the raw coexpression matrix for.

Returns:

the full, non-regressed matrix. If the matrix is not available event after attempted computation, returns null.

loadRegressedMatrix

@Nullable
DoubleMatrix<BioAssay,BioAssay> loadRegressedMatrix(ExpressionExperiment ee)

Load the regressed coexpression matrix for the given experiment.

Returns:

the regressed matrix if available, null might indicate that the is either no analysis or no regressed matrix, use hasAnalysis(ExpressionExperiment) to tell these apart.

loadBestMatrix

@Nullable
DoubleMatrix<BioAssay,BioAssay> loadBestMatrix(ExpressionExperiment ee)

Loads the analysis containing the coexpression matrices for the given experiment and converts the regressed coexpression matrix into a double matrix. If the analysis or the matrix does not exist, computes it. If there are problems loading or computing the regressed matrix (e.g. because the experiment has no experimental design), the full matrix is returned instead.

Parameters:

ee - the experiment to load the regressed coexpression matrix for.

Returns:

sample correlation matrix with major factors regressed out, if such matrix exists for the given experiment. If not, the full non-regressed matrix is returned. If no matrix is available event after attempted computation, returns null.

retrieveExisting

@Transactional(readOnly=true)
@Nullable
DoubleMatrix<BioAssay,BioAssay> retrieveExisting(ExpressionExperiment ee)

prepare

@Transactional(readOnly=true)
PreparedCoexMatrices prepare(ExpressionExperiment ee)

compute

@Transactional(isolation=SERIALIZABLE)
DoubleMatrix<BioAssay,BioAssay> compute(ExpressionExperiment ee,
                                              PreparedCoexMatrices matrices)

Computes sample correlation matrices for the given experiment. If the experiment already has any, they are removed. See SampleCoexpressionAnalysis for the description of the matrices that are computed.

Parameters:

ee - the experiment to create a sample correlation matrix for.

Returns:

the regressed coexpression matrix if available, otherwise the full

hasAnalysis

boolean hasAnalysis(ExpressionExperiment ee)

removeForExperiment

void removeForExperiment(ExpressionExperiment ee)

Removes all coexpression matrices for the given experiment.

Parameters:

ee - the experiment to remove the analysis for.