Package ubic.gemma.core.analysis.expression.diff

Interface DiffExAnalyzer

All Known Implementing Classes:

AbstractDifferentialExpressionAnalyzer, LinearModelAnalyzer

public interface DiffExAnalyzer

Author:

paul

Method Summary

Modifier and Type	Method	Description
Set<HitListSize>	computeHitListSizes(Collection<DifferentialExpressionAnalysisResult> results, Map<CompositeSequence,Collection<Gene>> probeToGeneMap)	Generate HitListSize entities that will be stored to count the number of diff.
ExperimentalFactor	determineInterceptFactor(Collection<ExperimentalFactor> factors, QuantitationType quantitationType)
int	getNumberOfGenesTested(Collection<DifferentialExpressionAnalysisResult> resultList, Map<CompositeSequence,Collection<Gene>> probeToGeneMap)	Utility method
Collection<DifferentialExpressionAnalysis>	run(ExpressionExperiment expressionExperiment, DifferentialExpressionAnalysisConfig config)
Collection<DifferentialExpressionAnalysis>	run(ExpressionExperiment expressionExperiment, ExpressionDataDoubleMatrix dmatrix, DifferentialExpressionAnalysisConfig config)	Allows entry of modified data matrices into the workflow.
DifferentialExpressionAnalysis	run(ExpressionExperimentSubSet subset, DifferentialExpressionAnalysisConfig config)	Note that normally when we run a subset analysis, the subsetting is done internally, so we pass in the expression experiment, not the subset.
void	setExpressionDataMatrixService(ExpressionDataMatrixService expressionDataMatrixService)	this is needed so we can alter this in tests

Method Detail

determineInterceptFactor

ExperimentalFactor determineInterceptFactor(Collection<ExperimentalFactor> factors,
                                            QuantitationType quantitationType)

run

Collection<DifferentialExpressionAnalysis> run(ExpressionExperiment expressionExperiment,
                                               DifferentialExpressionAnalysisConfig config)

Parameters:

expressionExperiment - the experiment

config - config

Returns:

analyses. There will be more than one if a subset factor is defined.

run

Collection<DifferentialExpressionAnalysis> run(ExpressionExperiment expressionExperiment,
                                               ExpressionDataDoubleMatrix dmatrix,
                                               DifferentialExpressionAnalysisConfig config)

Allows entry of modified data matrices into the workflow.

Parameters:

config - config

expressionExperiment - the experiment

dmatrix - D matrix

Returns:

analyses

computeHitListSizes

Set<HitListSize> computeHitListSizes(Collection<DifferentialExpressionAnalysisResult> results,
                                     Map<CompositeSequence,Collection<Gene>> probeToGeneMap)

Generate HitListSize entities that will be stored to count the number of diff. ex probes at various preset thresholds, to avoid wasting time generating these counts on the fly later. This is done automatically during analysis, so is just here to allow 'backfilling'.

Parameters:

probeToGeneMap - map

results - results

Returns:

hit list sizes

getNumberOfGenesTested

int getNumberOfGenesTested(Collection<DifferentialExpressionAnalysisResult> resultList,
                           Map<CompositeSequence,Collection<Gene>> probeToGeneMap)

Utility method

Parameters:

probeToGeneMap - map

resultList - result list

Returns:

number of genes tested

setExpressionDataMatrixService

void setExpressionDataMatrixService(ExpressionDataMatrixService expressionDataMatrixService)

this is needed so we can alter this in tests

Parameters:

expressionDataMatrixService - EE data matrix service

run

DifferentialExpressionAnalysis run(ExpressionExperimentSubSet subset,
                                   DifferentialExpressionAnalysisConfig config)

Note that normally when we run a subset analysis, the subsetting is done internally, so we pass in the expression experiment, not the subset. This method is used for exceptions to that.

Parameters:

subset - subset

config - config

Returns:

analysis