ubic.gemma.core.analysis.service

Interface ExpressionDataMatrixService

All Known Implementing Classes:

ExpressionDataMatrixServiceImpl

public interface ExpressionDataMatrixService

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

Author:

Paul

Method Summary

Modifier and Type	Method and Description
ExpressionDataDoubleMatrix	getFilteredMatrix(ExpressionExperiment ee, FilterConfig filterConfig) Provide a filtered expression data matrix.
ExpressionDataDoubleMatrix	getFilteredMatrix(ExpressionExperiment ee, FilterConfig filterConfig, Collection<ProcessedExpressionDataVector> dataVectors) Provide a filtered expression data matrix.
ExpressionDataDoubleMatrix	getFilteredMatrix(String arrayDesignName, FilterConfig filterConfig, Collection<ProcessedExpressionDataVector> dataVectors)
ExpressionDataDoubleMatrix	getProcessedExpressionDataMatrix(ExpressionExperiment ee)
ExpressionDataDoubleMatrix	getProcessedExpressionDataMatrix(ExpressionExperiment ee, QuantitationType quantitationType) Obtain a processed expression data matrix for a given quantitation type.
DoubleMatrix<Gene,ExpressionExperiment>	getRankMatrix(Collection<Gene> genes, Collection<ExpressionExperiment> ees, ProcessedExpressionDataVectorDao.RankMethod method)
ExpressionDataDoubleMatrix	getRawExpressionDataMatrix(ExpressionExperiment ee, QuantitationType quantitationType) Obtain a raw expression data matrix for a given quantitation type

Method Detail

getFilteredMatrix

@Nullable
ExpressionDataDoubleMatrix getFilteredMatrix(ExpressionExperiment ee,
                                                       FilterConfig filterConfig)
                                                throws FilteringException

Provide a filtered expression data matrix.

Parameters:

ee - the expression experiment.

filterConfig - the configuration.

Returns:

data matrix or null if the EE has no processed EVs

Throws:

FilteringException

getFilteredMatrix

ExpressionDataDoubleMatrix getFilteredMatrix(ExpressionExperiment ee,
                                             FilterConfig filterConfig,
                                             Collection<ProcessedExpressionDataVector> dataVectors)
                                      throws FilteringException

Provide a filtered expression data matrix.

Parameters:

ee - the expression experiment.

filterConfig - the configuration.

dataVectors - data vectors

Returns:

data matrix

Throws:

FilteringException

getFilteredMatrix

ExpressionDataDoubleMatrix getFilteredMatrix(String arrayDesignName,
                                             FilterConfig filterConfig,
                                             Collection<ProcessedExpressionDataVector> dataVectors)
                                      throws FilteringException

Throws:

FilteringException

getProcessedExpressionDataMatrix

@Nullable
ExpressionDataDoubleMatrix getProcessedExpressionDataMatrix(ExpressionExperiment ee)

Parameters:

ee - the expression experiment.

Returns:

matrix of preferred data, with all missing values masked or null if there are no processed EVs

getProcessedExpressionDataMatrix

@Nullable
ExpressionDataDoubleMatrix getProcessedExpressionDataMatrix(ExpressionExperiment ee,
                                                                      @Nullable
                                                                      QuantitationType quantitationType)

Obtain a processed expression data matrix for a given quantitation type.

Parameters:

quantitationType - the quantitation type, or null to pick the preferred one

getRawExpressionDataMatrix

ExpressionDataDoubleMatrix getRawExpressionDataMatrix(ExpressionExperiment ee,
                                                      @Nullable
                                                      QuantitationType quantitationType)

Obtain a raw expression data matrix for a given quantitation type

Parameters:

quantitationType - the quantitation type, or null to pick the preferred one

getRankMatrix

DoubleMatrix<Gene,ExpressionExperiment> getRankMatrix(Collection<Gene> genes,
                                                      Collection<ExpressionExperiment> ees,
                                                      ProcessedExpressionDataVectorDao.RankMethod method)