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

Method Details

getFilteredMatrix

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

Throws:

IllegalStateException - if there are no processed vectors

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

ExpressionDataDoubleMatrix getProcessedExpressionDataMatrix(ExpressionExperiment ee)

Obtain the processed expression data matrix for a given experiment.

getProcessedExpressionDataMatrix

ExpressionDataDoubleMatrix getProcessedExpressionDataMatrix(ExpressionExperiment ee,
 boolean thawAssays)

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

ExpressionDataDoubleMatrix getProcessedExpressionDataMatrix(ExpressionExperiment ee,
 List<BioAssay> samples)

getRawExpressionDataMatrix

ExpressionDataDoubleMatrix getRawExpressionDataMatrix(ExpressionExperiment ee,
 QuantitationType quantitationType)

Obtain a raw expression data matrix for a given quantitation type

Throws:

IllegalStateException - if there are no raw vectors for the given quantitation type

getRawExpressionDataMatrix

ExpressionDataDoubleMatrix getRawExpressionDataMatrix(ExpressionExperiment ee,
 List<BioAssay> samples,
 QuantitationType quantitationType)

getRankMatrix

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