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)
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> experimentsAnalyzed, boolean includeSubSets)	Get the differential expression results for the given gene that is in a specified set of experiments.
Collection<DifferentialExpressionValueObject>	getDifferentialExpression(Gene gene, BioAssaySet experimentAnalyzed, boolean includeSubSets, 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> experimentsAnalyzed, boolean includeSubSets)	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 Details

GeneDifferentialExpressionServiceImpl

@Autowired
public GeneDifferentialExpressionServiceImpl(DifferentialExpressionResultService differentialExpressionResultService)

Method Details

configExperimentalFactorValueObject

public ExperimentalFactorValueObject configExperimentalFactorValueObject(ExperimentalFactor ef)

Specified by:

configExperimentalFactorValueObject in interface GeneDifferentialExpressionService

getDifferentialExpression

public Collection<DifferentialExpressionValueObject> getDifferentialExpression(Gene gene,
 Collection<BioAssaySet> experimentsAnalyzed,
 boolean includeSubSets)

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

experimentsAnalyzed - set of experiments or subsets to search

includeSubSets - include subsets of the experiments analyzed

Returns:

DEA VOs

getDifferentialExpression

public Collection<DifferentialExpressionValueObject> getDifferentialExpression(Gene gene,
 BioAssaySet experimentAnalyzed,
 boolean includeSubSets,
 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

experimentAnalyzed - set of experiments to search

includeSubSets - include subsets of the experiment analyzed

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> experimentsAnalyzed,
 boolean includeSubSets)

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

experimentsAnalyzed - active ees

includeSubSets -

Returns:

diff exp. analysis meta VO