Package ubic.gemma.persistence.service.analysis.expression.diff

Interface DifferentialExpressionResultService

All Superinterfaces:

BaseReadOnlyService<DifferentialExpressionAnalysisResult>

All Known Implementing Classes:

DifferentialExpressionResultServiceImpl

public interface DifferentialExpressionResultService
extends BaseReadOnlyService<DifferentialExpressionAnalysisResult>

Main entry point to retrieve differential expression data.

Author:

kelsey

Method Summary

Modifier and Type	Method	Description
Map<ExpressionExperimentValueObject,List<DifferentialExpressionValueObject>>	find(Collection<Long> experimentsAnalyzed, double threshold, int limit)	Given a list of experiments and a threshold value finds all the probes that met the cut off in the given experiments
Map<ExpressionExperimentValueObject,List<DifferentialExpressionValueObject>>	find(Gene gene)	Returns a map of a collection of DifferentialExpressionAnalysisResults keyed by ExpressionExperiment.
Map<ExpressionExperimentValueObject,List<DifferentialExpressionValueObject>>	find(Gene gene, double threshold, int limit)	Find differential expression for a gene, exceeding a given significance level (using the corrected pvalue field)
Map<ExpressionExperimentValueObject,List<DifferentialExpressionValueObject>>	find(Gene gene, Collection<Long> experimentsAnalyzed)	Returns a map of a collection of DifferentialExpressionAnalysisResults keyed by ExpressionExperiment.
Map<ExpressionExperimentValueObject,List<DifferentialExpressionValueObject>>	find(Gene gene, Collection<Long> experimentsAnalyzed, double threshold, int limit)	Find differential expression for a gene in given data sets, exceeding a given significance level (using the corrected pvalue field)
List<DifferentialExpressionAnalysisResult>	findByGeneAndExperimentAnalyzed(Gene gene, Collection<Long> experimentAnalyzedIds, Map<DifferentialExpressionAnalysisResult,Long> sourceExperimentIdMap, Map<DifferentialExpressionAnalysisResult,Long> experimentAnalyzedIdMap, Map<DifferentialExpressionAnalysisResult,Baseline> baselineMap, double threshold, boolean keepNonSpecific, boolean initializeFactorValues)
Map<Long,Map<Long,DiffExprGeneSearchResult>>	findDiffExAnalysisResultIdsInResultSets(Collection<DiffExResultSetSummaryValueObject> resultSets, Collection<Long> geneIds)	Retrieve differential expression results in bulk.
List<DifferentialExpressionValueObject>	findInResultSet(ExpressionAnalysisResultSet ar, Double threshold, int maxResultsToReturn, int minNumberOfResults)
Map<Long,ContrastsValueObject>	loadContrastDetailsForResults(Collection<Long> ids)

Methods inherited from interface ubic.gemma.persistence.service.BaseReadOnlyService

countAll, find, findOrFail, getElementClass, load, load, loadAll, loadOrFail, loadOrFail, loadOrFail, loadOrFail

Method Detail

findByGeneAndExperimentAnalyzed

@Secured("IS_AUTHENTICATED_ANONYMOUSLY")
List<DifferentialExpressionAnalysisResult> findByGeneAndExperimentAnalyzed(Gene gene,
                                                                           Collection<Long> experimentAnalyzedIds,
                                                                           Map<DifferentialExpressionAnalysisResult,Long> sourceExperimentIdMap,
                                                                           Map<DifferentialExpressionAnalysisResult,Long> experimentAnalyzedIdMap,
                                                                           Map<DifferentialExpressionAnalysisResult,Baseline> baselineMap,
                                                                           double threshold,
                                                                           boolean keepNonSpecific,
                                                                           boolean initializeFactorValues)

See Also:

DifferentialExpressionResultDao.findByGeneAndExperimentAnalyzed(Gene, Collection, boolean, Map, Map, Map, double, boolean, boolean)

find

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_VALUE_OBJECT_MAP_READ"})
Map<ExpressionExperimentValueObject,List<DifferentialExpressionValueObject>> find(Collection<Long> experimentsAnalyzed,
                                                                                        double threshold,
                                                                                        int limit)

Given a list of experiments and a threshold value finds all the probes that met the cut off in the given experiments

Parameters:

experimentsAnalyzed - ees

threshold - threshold

limit - limit

Returns:

map to diff ex VOs

find

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_VALUE_OBJECT_MAP_READ"})
Map<ExpressionExperimentValueObject,List<DifferentialExpressionValueObject>> find(Gene gene)

Returns a map of a collection of DifferentialExpressionAnalysisResults keyed by ExpressionExperiment.

Parameters:

gene - gene

Returns:

map to diff ex VOs

find

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_VALUE_OBJECT_MAP_READ"})
Map<ExpressionExperimentValueObject,List<DifferentialExpressionValueObject>> find(Gene gene,
                                                                                        Collection<Long> experimentsAnalyzed)

Returns a map of a collection of DifferentialExpressionAnalysisResults keyed by ExpressionExperiment.

Parameters:

experimentsAnalyzed - ees

gene - gene

Returns:

map to diff ex VOs

find

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_VALUE_OBJECT_MAP_READ"})
Map<ExpressionExperimentValueObject,List<DifferentialExpressionValueObject>> find(Gene gene,
                                                                                        Collection<Long> experimentsAnalyzed,
                                                                                        double threshold,
                                                                                        int limit)

Find differential expression for a gene in given data sets, exceeding a given significance level (using the corrected pvalue field)

Parameters:

experimentsAnalyzed - ees

threshold - threshold

limit - limit

gene - gene

Returns:

map to diff ex VOs

find

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_VALUE_OBJECT_MAP_READ"})
Map<ExpressionExperimentValueObject,List<DifferentialExpressionValueObject>> find(Gene gene,
                                                                                        double threshold,
                                                                                        int limit)

Find differential expression for a gene, exceeding a given significance level (using the corrected pvalue field)

Parameters:

gene - gene

threshold - threshold

limit - limit

Returns:

map to diff ex VOs

findDiffExAnalysisResultIdsInResultSets

Map<Long,Map<Long,DiffExprGeneSearchResult>> findDiffExAnalysisResultIdsInResultSets(Collection<DiffExResultSetSummaryValueObject> resultSets,
                                                                                                 Collection<Long> geneIds)

Retrieve differential expression results in bulk. This is an important method for the differential expression interfaces.

Parameters:

geneIds - gene ids

resultSets - result sets

Returns:

map of resultset IDs to map of gene id to differential expression results.

findInResultSet

List<DifferentialExpressionValueObject> findInResultSet(ExpressionAnalysisResultSet ar,
                                                        Double threshold,
                                                        int maxResultsToReturn,
                                                        int minNumberOfResults)

loadContrastDetailsForResults

Map<Long,ContrastsValueObject> loadContrastDetailsForResults(Collection<Long> ids)

Parameters:

ids - ids

Returns:

map of result to contrasts value object.