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

Class LinearModelAnalyzer

java.lang.Object

ubic.gemma.core.analysis.expression.diff.AbstractAnalyzer

ubic.gemma.core.analysis.expression.diff.AbstractDifferentialExpressionAnalyzer

ubic.gemma.core.analysis.expression.diff.LinearModelAnalyzer

All Implemented Interfaces:

org.springframework.beans.factory.DisposableBean, DiffExAnalyzer

@Component
@Scope("prototype")
public class LinearModelAnalyzer
extends AbstractDifferentialExpressionAnalyzer
implements org.springframework.beans.factory.DisposableBean

Handles fitting linear models with continuous or fixed-level covariates. Data are always log-transformed. Interactions can be included if a DifferentialExpressionAnalysisConfig is passed as an argument to 'run'. Currently we only support interactions if there are two factors in the model (no more). One factor can be constant (the same value for all samples); such a factor will be analyzed by looking at the intercept in the fitted model. This is only appropriate for 'non-reference' designs on ratiometric arrays. This also supports subsetting the data based on a factor. For example, a data set with "tissue" as a factor could be analyzed per-tissue rather than with tissue as a covariate. This only handles the analysis, not the persistence or output of the results.

Author:

paul

Field Summary

Fields inherited from class ubic.gemma.core.analysis.expression.diff.AbstractAnalyzer

compositeSequenceService, expressionDataMatrixService

Constructor Summary

Constructors

Constructor	Description
LinearModelAnalyzer()

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.
static BioAssayDimension	createBADMap(List<BioMaterial> columnsToUse)	This bioAssayDimension shouldn't get persisted; it is only for dealing with subset diff ex.
void	destroy()
ExperimentalFactor	determineInterceptFactor(Collection<ExperimentalFactor> factors, QuantitationType quantitationType)	Determine if any factor should be treated as the intercept term.
int	getNumberOfGenesTested(Collection<DifferentialExpressionAnalysisResult> resultList, Map<CompositeSequence,Collection<Gene>> probeToGeneMap)	Utility method
static DoubleMatrix<String,String>	makeDataMatrix(ObjectMatrix<String,String,Object> designMatrix, DoubleMatrix<CompositeSequence,BioMaterial> namedMatrix)	Convert the data into a string-keyed matrix.
static void	populateFactorValuesFromBASet(BioAssaySet ee, ExperimentalFactor f, Collection<FactorValue> fvs)
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.

Methods inherited from class ubic.gemma.core.analysis.expression.diff.AbstractAnalyzer

setExpressionDataMatrixService

Methods inherited from class java.lang.Object

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

Methods inherited from interface ubic.gemma.core.analysis.expression.diff.DiffExAnalyzer

setExpressionDataMatrixService

Constructor Detail

LinearModelAnalyzer

public LinearModelAnalyzer()

Method Detail

populateFactorValuesFromBASet

public static void populateFactorValuesFromBASet(BioAssaySet ee,
                                                 ExperimentalFactor f,
                                                 Collection<FactorValue> fvs)

makeDataMatrix

public static DoubleMatrix<String,String> makeDataMatrix(ObjectMatrix<String,String,Object> designMatrix,
                                                               DoubleMatrix<CompositeSequence,BioMaterial> namedMatrix)

Convert the data into a string-keyed matrix. Assumes that the row names of the designMatrix are concordant with the column names of the namedMatrix

createBADMap

public static BioAssayDimension createBADMap(List<BioMaterial> columnsToUse)

This bioAssayDimension shouldn't get persisted; it is only for dealing with subset diff ex. analyses.

Parameters:

columnsToUse - columns to use

Returns:

bio assay dimension

destroy

public void destroy()
             throws Exception

Specified by:

destroy in interface org.springframework.beans.factory.DisposableBean

Throws:

Exception

determineInterceptFactor

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

Determine if any factor should be treated as the intercept term.

Specified by:

determineInterceptFactor in interface DiffExAnalyzer

computeHitListSizes

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

Description copied from interface: DiffExAnalyzer

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'.

Specified by:

computeHitListSizes in interface DiffExAnalyzer

Parameters:

results - results

probeToGeneMap - map

Returns:

hit list sizes

getNumberOfGenesTested

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

Description copied from interface: DiffExAnalyzer

Utility method

Specified by:

getNumberOfGenesTested in interface DiffExAnalyzer

Parameters:

resultList - result list

probeToGeneMap - map

Returns:

number of genes tested

run

public DifferentialExpressionAnalysis run(ExpressionExperimentSubSet subset,
                                          DifferentialExpressionAnalysisConfig config)

Description copied from interface: DiffExAnalyzer

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.

Specified by:

run in interface DiffExAnalyzer

Parameters:

subset - subset

config - config

Returns:

analysis

run

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

Specified by:

run in interface DiffExAnalyzer

Specified by:

run in class AbstractDifferentialExpressionAnalyzer

Parameters:

expressionExperiment - the experiment

config - config

Returns:

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

run

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

Description copied from interface: DiffExAnalyzer

Allows entry of modified data matrices into the workflow.

Specified by:

run in interface DiffExAnalyzer

Specified by:

run in class AbstractDifferentialExpressionAnalyzer

Parameters:

expressionExperiment - the experiment

dmatrix - D matrix

config - config

Returns:

analyses