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

Class GeneDifferentialExpressionServiceImpl

java.lang.Object

ubic.gemma.core.analysis.expression.diff.GeneDifferentialExpressionServiceImpl

All Implemented Interfaces:

GeneDifferentialExpressionService

@Component
public class GeneDifferentialExpressionServiceImpl
extends Object
implements GeneDifferentialExpressionService

Provides access to DifferentialExpressionAnalysisResults and meta-analysis results.

Author:

keshav, anton

Field Summary

Fields inherited from interface ubic.gemma.core.analysis.expression.diff.GeneDifferentialExpressionService

PVALUE_CLIP_THRESHOLD

Constructor Summary

Constructors

Constructor	Description
GeneDifferentialExpressionServiceImpl(DifferentialExpressionResultService differentialExpressionResultService)

Method Summary

Modifier and Type	Method	Description
ExperimentalFactorValueObject	configExperimentalFactorValueObject(ExperimentalFactor ef)
ExpressionExperimentValueObject	configExpressionExperimentValueObject(ExpressionExperimentValueObject ee)
Collection<DifferentialExpressionValueObject>	getDifferentialExpression(Gene gene, double threshold, int limit)	Get the differential expression results for the given gene across all datasets.
Collection<DifferentialExpressionValueObject>	getDifferentialExpression(Gene gene, double threshold, Collection<DiffExpressionSelectedFactorCommand> factorMap)	Get differential expression for a gene, constrained to a specific set of factors.
Collection<DifferentialExpressionValueObject>	getDifferentialExpression(Gene gene, Collection<BioAssaySet> ees)	Get the differential expression results for the given gene that is in a specified set of experiments.
Collection<DifferentialExpressionValueObject>	getDifferentialExpression(Gene gene, BioAssaySet ee, double threshold, int limit)	Get the differential expression results for the given gene that is in a specified set of experiments.
DifferentialExpressionMetaAnalysisValueObject	getDifferentialExpressionMetaAnalysis(double threshold, Gene g, Map<Long,Long> eeFactorsMap, Collection<BioAssaySet> activeExperiments)	Get the differential expression analysis results for the gene in the activeExperiments.

Methods inherited from class java.lang.Object

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

Constructor Detail

GeneDifferentialExpressionServiceImpl

@Autowired
public GeneDifferentialExpressionServiceImpl(DifferentialExpressionResultService differentialExpressionResultService)

Method Detail

configExperimentalFactorValueObject

public ExperimentalFactorValueObject configExperimentalFactorValueObject(ExperimentalFactor ef)

Specified by:

configExperimentalFactorValueObject in interface GeneDifferentialExpressionService

configExpressionExperimentValueObject

public ExpressionExperimentValueObject configExpressionExperimentValueObject(ExpressionExperimentValueObject ee)

Specified by:

configExpressionExperimentValueObject in interface GeneDifferentialExpressionService

getDifferentialExpression

public Collection<DifferentialExpressionValueObject> getDifferentialExpression(Gene gene,
                                                                               Collection<BioAssaySet> ees)

Description copied from interface: GeneDifferentialExpressionService

Get the differential expression results for the given gene that is in a specified set of experiments.

Specified by:

getDifferentialExpression in interface GeneDifferentialExpressionService

Parameters:

gene - : gene of interest

ees - : set of experiments to search

Returns:

DEA VOs

getDifferentialExpression

public Collection<DifferentialExpressionValueObject> getDifferentialExpression(Gene gene,
                                                                               BioAssaySet ee,
                                                                               double threshold,
                                                                               int limit)

Description copied from interface: GeneDifferentialExpressionService

Get the differential expression results for the given gene that is in a specified set of experiments.

Specified by:

getDifferentialExpression in interface GeneDifferentialExpressionService

Parameters:

gene - : gene of interest

ee - : set of experiments to search

threshold - : the cutoff to determine if diff expressed

limit - : the maximum number of results to return (null for all)

Returns:

DEA VOs

getDifferentialExpression

public Collection<DifferentialExpressionValueObject> getDifferentialExpression(Gene gene,
                                                                               double threshold,
                                                                               Collection<DiffExpressionSelectedFactorCommand> factorMap)

Description copied from interface: GeneDifferentialExpressionService

Get differential expression for a gene, constrained to a specific set of factors. Note that interactions are ignored, only main effects (the factorMap can only have one factor per experiment)

Specified by:

getDifferentialExpression in interface GeneDifferentialExpressionService

Parameters:

gene - gene

threshold - threshold

factorMap - factor map

Returns:

DEA VOs

getDifferentialExpression

public Collection<DifferentialExpressionValueObject> getDifferentialExpression(Gene gene,
                                                                               double threshold,
                                                                               int limit)

Description copied from interface: GeneDifferentialExpressionService

Get the differential expression results for the given gene across all datasets.

Specified by:

getDifferentialExpression in interface GeneDifferentialExpressionService

Parameters:

gene - gene

threshold - threshold

limit - limit

Returns:

DEA VOs

getDifferentialExpressionMetaAnalysis

public DifferentialExpressionMetaAnalysisValueObject getDifferentialExpressionMetaAnalysis(double threshold,
                                                                                           Gene g,
                                                                                           Map<Long,Long> eeFactorsMap,
                                                                                           Collection<BioAssaySet> activeExperiments)

Description copied from interface: GeneDifferentialExpressionService

Get the differential expression analysis results for the gene in the activeExperiments.

Specified by:

getDifferentialExpressionMetaAnalysis in interface GeneDifferentialExpressionService

Parameters:

threshold - threshold

g - gene

eeFactorsMap - factor map

activeExperiments - active ees

Returns:

diff exp. analysis meta VO