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

Interface ExpressionAnalysisResultSetDao

All Superinterfaces:

AnalysisResultSetDao<DifferentialExpressionAnalysisResult,ExpressionAnalysisResultSet>, BaseDao<ExpressionAnalysisResultSet>, BaseVoEnabledDao<ExpressionAnalysisResultSet,DifferentialExpressionAnalysisResultSetValueObject>, FilteringDao<ExpressionAnalysisResultSet>, FilteringVoEnabledDao<ExpressionAnalysisResultSet,DifferentialExpressionAnalysisResultSetValueObject>

All Known Implementing Classes:

ExpressionAnalysisResultSetDaoImpl

public interface ExpressionAnalysisResultSetDao
extends AnalysisResultSetDao<DifferentialExpressionAnalysisResult,ExpressionAnalysisResultSet>, FilteringVoEnabledDao<ExpressionAnalysisResultSet,DifferentialExpressionAnalysisResultSetValueObject>

See Also:

• ExpressionAnalysisResultSet

Method Summary

Modifier and Type	Method	Description
boolean	canDelete(DifferentialExpressionAnalysis differentialExpressionAnalysis)
long	countResults(ExpressionAnalysisResultSet ears)	Count the number of results in a given result set.
long	countResults(ExpressionAnalysisResultSet ears, double threshold)	Count the number of results in a given result set below a given corrected P-value threshold.
Slice<DifferentialExpressionAnalysisResultSetValueObject>	findByBioAssaySetInAndDatabaseEntryInLimit(Collection<BioAssaySet> bioAssaySets, Collection<DatabaseEntry> databaseEntries, Filters filters, int offset, int limit, Sort sort)	Retrieve result sets associated to a set of BioAssaySet and external database entries.
Baseline	getBaseline(ExpressionAnalysisResultSet ears)	Retrieve the baseline for the given result set.
Map<ExpressionAnalysisResultSet,Baseline>	getBaselinesForInteractions(Collection<ExpressionAnalysisResultSet> resultSets, boolean initializeFactorValues)	Retrieve baselines for all the given result sets representing factor interactions.
Map<Long,Baseline>	getBaselinesForInteractionsByIds(Collection<Long> ids, boolean initializeFactorValues)	Retrieve baselines using result set IDs representing factor interactions.
Histogram	loadPvalueDistribution(ExpressionAnalysisResultSet resultSet)	Obtain a histogram of the P-value distribution for a given result set.
Map<Long,Set<Gene>>	loadResultToGenesMap(ExpressionAnalysisResultSet resultSet, boolean queryByResult)	Load a DifferentialExpressionAnalysisResult to Gene multi-map.
DifferentialExpressionAnalysisResultSetValueObject	loadValueObjectWithResults(ExpressionAnalysisResultSet resultSet, boolean includeFactorValuesInContrasts, boolean queryGenesByResult, boolean includeTaxonInGenes)	Load an analysis result set with its all of its associated results.
ExpressionAnalysisResultSet	loadWithResultsAndContrasts(Long id)	Load an analysis result set with its all of its associated results.
ExpressionAnalysisResultSet	loadWithResultsAndContrasts(Long id, double threshold, int offset, int limit)	Load a slice of an analysis result set with a corrected P-value threshold.
ExpressionAnalysisResultSet	loadWithResultsAndContrasts(Long id, int offset, int limit)	Load a slice of an analysis result set.
void	thaw(ExpressionAnalysisResultSet ears)	Initialize the analysis and subset factor vale.

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

countAll, create, create, find, findOrCreate, getElementClass, getIdentifierPropertyName, load, load, loadAll, loadReference, loadReference, reload, reload, remove, remove, remove, save, save, streamAll, streamAll, update, update

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

loadAllValueObjects, loadValueObject, loadValueObjectById, loadValueObjects, loadValueObjectsByIds

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

count, getFilter, getFilter, getFilter, getFilter, getFilter, getFilter, getFilterableProperties, getFilterablePropertyAllowedValues, getFilterablePropertyDescription, getFilterablePropertyIsUsingSubquery, getFilterablePropertyType, getSort, load, load, loadIds

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

loadValueObjects, loadValueObjects

Method Details

loadWithResultsAndContrasts

@Nullable
ExpressionAnalysisResultSet loadWithResultsAndContrasts(Long id)

Load an analysis result set with its all of its associated results.

Parameters:

id - the ID of the analysis result set

Returns:

the analysis result set with its associated results, or null if not found

loadWithResultsAndContrasts

@Nullable
ExpressionAnalysisResultSet loadWithResultsAndContrasts(Long id,
 int offset,
 int limit)

Load a slice of an analysis result set.

Results are sorted by ascending correct P-value.

Parameters:

offset - an offset of results to load

limit - a limit of results to load, or -1 to load all results starting at offset

See Also:

• loadWithResultsAndContrasts(Long)

loadWithResultsAndContrasts

@Nullable
ExpressionAnalysisResultSet loadWithResultsAndContrasts(Long id,
 double threshold,
 int offset,
 int limit)

Load a slice of an analysis result set with a corrected P-value threshold.

Important note: when using a threshold, results with null P-values will not be included, thus setting the threshold to 1.0 is not equivalent to loadWithResultsAndContrasts(Long, int, int).

Parameters:

threshold - corrected P-value maximum threshold (inclusive)

canDelete

boolean canDelete(DifferentialExpressionAnalysis differentialExpressionAnalysis)

loadValueObjectWithResults

DifferentialExpressionAnalysisResultSetValueObject loadValueObjectWithResults(ExpressionAnalysisResultSet resultSet,
 boolean includeFactorValuesInContrasts,
 boolean queryGenesByResult,
 boolean includeTaxonInGenes)

Load an analysis result set with its all of its associated results.

Parameters:

includeFactorValuesInContrasts - include complete FV in the contrasts, only IDs are displayed if false

queryGenesByResult - query genes by results instead of result set, this is considerably faster if the results are sliced (i.e. from loadWithResultsAndContrasts(Long, int, int))

includeTaxonInGenes - include complete taxon in the contrasts, only the ID is displayed if false

See Also:

• BaseVoEnabledDao.loadValueObject(Identifiable)
• loadResultToGenesMap(ExpressionAnalysisResultSet, boolean)

loadResultToGenesMap

Map<Long,Set<Gene>> loadResultToGenesMap(ExpressionAnalysisResultSet resultSet,
 boolean queryByResult)

Load a DifferentialExpressionAnalysisResult to Gene multi-map.

This is much faster than navigating through the probe's alignments, transcripts and then genes as it uses the internal GENE2CS table described in TableMaintenanceUtil.updateGene2CsEntries().

Note: Not all probes have associated genes, so you should use Map.getOrDefault(Object, Object) with an empty collection to handle this case.

Parameters:

queryByResult - query by results instead of result set, this is considerably faster if the results are sliced (i.e. from loadWithResultsAndContrasts(Long, int, int))

findByBioAssaySetInAndDatabaseEntryInLimit

Slice<DifferentialExpressionAnalysisResultSetValueObject> findByBioAssaySetInAndDatabaseEntryInLimit(@Nullable
 Collection<BioAssaySet> bioAssaySets,
 @Nullable
 Collection<DatabaseEntry> databaseEntries,
 @Nullable
 Filters filters,
 int offset,
 int limit,
 @Nullable
 Sort sort)

Retrieve result sets associated to a set of BioAssaySet and external database entries.

Parameters:

bioAssaySets - related BioAssaySet, or any if null

databaseEntries - related external identifier associated to the BioAssaySet, or any if null

filters - filters for restricting results

limit - maximum number of results to return

sort - field and direction by which the collection is ordered

thaw

void thaw(ExpressionAnalysisResultSet ears)

Initialize the analysis and subset factor vale.

countResults

long countResults(ExpressionAnalysisResultSet ears)

Count the number of results in a given result set.

countResults

long countResults(ExpressionAnalysisResultSet ears,
 double threshold)

Count the number of results in a given result set below a given corrected P-value threshold.

getBaseline

@Nullable
Baseline getBaseline(ExpressionAnalysisResultSet ears)

Retrieve the baseline for the given result set.

Factor values are always initialized.

Returns:

a baseline, or null if none could be determined for the given result set

getBaselinesForInteractions

Map<ExpressionAnalysisResultSet,Baseline> getBaselinesForInteractions(Collection<ExpressionAnalysisResultSet> resultSets,
 boolean initializeFactorValues)

Retrieve baselines for all the given result sets representing factor interactions.

Parameters:

initializeFactorValues - whether to initialize factor values

getBaselinesForInteractionsByIds

Map<Long,Baseline> getBaselinesForInteractionsByIds(Collection<Long> ids,
 boolean initializeFactorValues)

Retrieve baselines using result set IDs representing factor interactions.

Parameters:

initializeFactorValues - whether to initialize factor values

loadPvalueDistribution

@Nullable
Histogram loadPvalueDistribution(ExpressionAnalysisResultSet resultSet)

Obtain a histogram of the P-value distribution for a given result set.