Uses of Class
ubic.gemma.model.expression.bioAssay.BioAssay
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Uses of BioAssay in ubic.gemma.core.analysis.preprocess
Methods in ubic.gemma.core.analysis.preprocess that return BioAssay Modifier and Type Method Description BioAssay
OutlierDetails. getBioAssay()
Method parameters in ubic.gemma.core.analysis.preprocess with type arguments of type BioAssay Modifier and Type Method Description Collection<OutlierDetails>
OutlierDetectionService. identifyOutliersByMedianCorrelation(DoubleMatrix<BioAssay,BioAssay> cormat)
Identify outliers by sorting by median, then looking for non-overlap of first quartile-second quartile range This is exposed for efficiency in geeq score calculation, use this#identifyOutliers(ExpressionExperiment, boolean, boolean) to have the correlation matrix computed correctly for you.Collection<OutlierDetails>
OutlierDetectionService. identifyOutliersByMedianCorrelation(DoubleMatrix<BioAssay,BioAssay> cormat)
Identify outliers by sorting by median, then looking for non-overlap of first quartile-second quartile range This is exposed for efficiency in geeq score calculation, use this#identifyOutliers(ExpressionExperiment, boolean, boolean) to have the correlation matrix computed correctly for you.Collection<OutlierDetails>
OutlierDetectionServiceImpl. identifyOutliersByMedianCorrelation(DoubleMatrix<BioAssay,BioAssay> cormat)
Collection<OutlierDetails>
OutlierDetectionServiceImpl. identifyOutliersByMedianCorrelation(DoubleMatrix<BioAssay,BioAssay> cormat)
Constructors in ubic.gemma.core.analysis.preprocess with parameters of type BioAssay Constructor Description OutlierDetails(BioAssay bioAssay)
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Uses of BioAssay in ubic.gemma.core.analysis.preprocess.batcheffects
Methods in ubic.gemma.core.analysis.preprocess.batcheffects that return types with arguments of type BioAssay Modifier and Type Method Description static Map<String,BioAssay>
BatchInfoParser. getAccessionToBioAssayMap(ExpressionExperiment ee)
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Uses of BioAssay in ubic.gemma.core.analysis.service
Method parameters in ubic.gemma.core.analysis.service with type arguments of type BioAssay Modifier and Type Method Description void
OutlierFlaggingService. markAsMissing(Collection<BioAssay> assaysToRemove)
This does not actually remove the sample; rather, it sets all values to "missing" in the processed data.void
OutlierFlaggingServiceImpl. markAsMissing(Collection<BioAssay> bioAssays)
void
OutlierFlaggingService. unmarkAsMissing(Collection<BioAssay> bioAssays)
Reverts the action of markAsMissing.void
OutlierFlaggingServiceImpl. unmarkAsMissing(Collection<BioAssay> bioAssays)
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Uses of BioAssay in ubic.gemma.core.datastructure.matrix
Methods in ubic.gemma.core.datastructure.matrix that return types with arguments of type BioAssay Modifier and Type Method Description Collection<BioAssay>
BaseExpressionDataMatrix. getBioAssaysForColumn(int index)
Collection<BioAssay>
ExpressionDataMatrix. getBioAssaysForColumn(int index)
static <R> DoubleMatrix<R,BioAssay>
ExpressionDataMatrixColumnSort. orderByExperimentalDesign(DoubleMatrix<R,BioAssay> mat)
static <R> DoubleMatrix<R,BioAssay>
ExpressionDataMatrixColumnSort. orderByExperimentalDesign(DoubleMatrix<R,BioAssay> mat, ExperimentalFactor primaryFactor)
Methods in ubic.gemma.core.datastructure.matrix with parameters of type BioAssay Modifier and Type Method Description Object
EmptyExpressionMatrix. get(CompositeSequence designElement, BioAssay bioAssay)
Boolean
ExpressionDataBooleanMatrix. get(CompositeSequence designElement, BioAssay bioAssay)
Double
ExpressionDataDoubleMatrix. get(CompositeSequence designElement, BioAssay bioAssay)
Integer
ExpressionDataIntegerMatrix. get(CompositeSequence designElement, BioAssay bioAssay)
T
ExpressionDataMatrix. get(CompositeSequence designElement, BioAssay bioAssay)
Access a single value of the matrix.String
ExpressionDataStringMatrix. get(CompositeSequence designElement, BioAssay bioAssay)
Object[]
EmptyExpressionMatrix. getColumn(BioAssay bioAssay)
Boolean[]
ExpressionDataBooleanMatrix. getColumn(BioAssay bioAssay)
Double[]
ExpressionDataDoubleMatrix. getColumn(BioAssay bioAssay)
Integer[]
ExpressionDataIntegerMatrix. getColumn(BioAssay bioAssay)
T[]
ExpressionDataMatrix. getColumn(BioAssay bioAssay)
Access a single column of the matrix.String[]
ExpressionDataStringMatrix. getColumn(BioAssay bioAssay)
void
ExpressionDataDoubleMatrix. set(CompositeSequence designElement, BioAssay bioAssay, Double value)
Method parameters in ubic.gemma.core.datastructure.matrix with type arguments of type BioAssay Modifier and Type Method Description static String
ExpressionDataWriterUtils. constructBioAssayName(BioMaterial bioMaterial, Collection<BioAssay> bioAssays)
Object[][]
EmptyExpressionMatrix. getColumns(List<BioAssay> bioAssays)
Boolean[][]
ExpressionDataBooleanMatrix. getColumns(List<BioAssay> bioAssays)
Double[][]
ExpressionDataDoubleMatrix. getColumns(List<BioAssay> bioAssays)
Integer[][]
ExpressionDataIntegerMatrix. getColumns(List<BioAssay> bioAssays)
T[][]
ExpressionDataMatrix. getColumns(List<BioAssay> bioAssays)
Access a submatrix slice by columnsString[][]
ExpressionDataStringMatrix. getColumns(List<BioAssay> bioAssays)
static String
ExpressionDataWriterUtils. getExternalId(BioMaterial bioMaterial, Collection<BioAssay> bioAssays)
static <R> DoubleMatrix<R,BioAssay>
ExpressionDataMatrixColumnSort. orderByExperimentalDesign(DoubleMatrix<R,BioAssay> mat)
static <R> DoubleMatrix<R,BioAssay>
ExpressionDataMatrixColumnSort. orderByExperimentalDesign(DoubleMatrix<R,BioAssay> mat, ExperimentalFactor primaryFactor)
void
ExperimentalDesignWriter. write(Writer writer, ExpressionExperiment ee, Collection<BioAssay> bioAssays, boolean writeBaseHeader, boolean writeHeader)
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Uses of BioAssay in ubic.gemma.core.loader.expression
Methods in ubic.gemma.core.loader.expression that return BioAssay Modifier and Type Method Description static BioAssay
AffyPowerToolsProbesetSummarize. matchBioAssayToCelFileName(Map<String,BioAssay> bmap, String fileName)
Method parameters in ubic.gemma.core.loader.expression with type arguments of type BioAssay Modifier and Type Method Description static BioAssay
AffyPowerToolsProbesetSummarize. matchBioAssayToCelFileName(Map<String,BioAssay> bmap, String fileName)
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Uses of BioAssay in ubic.gemma.core.loader.expression.arrayDesign
Methods in ubic.gemma.core.loader.expression.arrayDesign that return types with arguments of type BioAssay Modifier and Type Method Description static Map<BioAssay,String>
AffyChipTypeExtractor. getChipTypes(ExpressionExperiment ee, Collection<LocalFile> files)
Extract a string like "Rat230_2" from CEL files. -
Uses of BioAssay in ubic.gemma.model.expression.bioAssay
Methods in ubic.gemma.model.expression.bioAssay that return BioAssay Modifier and Type Method Description static BioAssay
BioAssay.Factory. newInstance()
static BioAssay
BioAssay.Factory. newInstance(String name)
Method parameters in ubic.gemma.model.expression.bioAssay with type arguments of type BioAssay Modifier and Type Method Description static Collection<BioAssayValueObject>
BioAssayValueObject. convert2ValueObjects(Collection<BioAssay> bioAssays)
Constructors in ubic.gemma.model.expression.bioAssay with parameters of type BioAssay Constructor Description BioAssayValueObject(BioAssay bioAssay, boolean basic)
BioAssayValueObject(BioAssay bioAssay, boolean basic, boolean predictedOutlier)
BioAssayValueObject(BioAssay bioAssay, Map<Long,ArrayDesignValueObject> arrayDesignValueObjectsById, boolean basic)
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Uses of BioAssay in ubic.gemma.model.expression.bioAssayData
Methods in ubic.gemma.model.expression.bioAssayData that return types with arguments of type BioAssay Modifier and Type Method Description List<BioAssay>
BioAssayDimension. getBioAssays()
Method parameters in ubic.gemma.model.expression.bioAssayData with type arguments of type BioAssay Modifier and Type Method Description static BioAssayDimension
BioAssayDimension.Factory. newInstance(String name, String description, List<BioAssay> bioAssays)
void
BioAssayDimension. setBioAssays(List<BioAssay> bioAssays)
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Uses of BioAssay in ubic.gemma.model.expression.biomaterial
Methods in ubic.gemma.model.expression.biomaterial that return types with arguments of type BioAssay Modifier and Type Method Description Set<BioAssay>
BioMaterial. getBioAssaysUsedIn()
Method parameters in ubic.gemma.model.expression.biomaterial with type arguments of type BioAssay Modifier and Type Method Description void
BioMaterial. setBioAssaysUsedIn(Set<BioAssay> bioAssaysUsedIn)
Constructors in ubic.gemma.model.expression.biomaterial with parameters of type BioAssay Constructor Description BioMaterialValueObject(BioMaterial bm, BioAssay ba)
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Uses of BioAssay in ubic.gemma.model.expression.experiment
Methods in ubic.gemma.model.expression.experiment that return types with arguments of type BioAssay Modifier and Type Method Description Set<BioAssay>
BioAssaySet. getBioAssays()
Set<BioAssay>
ExpressionExperiment. getBioAssays()
Method parameters in ubic.gemma.model.expression.experiment with type arguments of type BioAssay Modifier and Type Method Description void
BioAssaySet. setBioAssays(Set<BioAssay> bioAssays)
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Uses of BioAssay in ubic.gemma.persistence.service.analysis.expression.sampleCoexpression
Methods in ubic.gemma.persistence.service.analysis.expression.sampleCoexpression that return types with arguments of type BioAssay Modifier and Type Method Description DoubleMatrix<BioAssay,BioAssay>
SampleCoexpressionAnalysisService. compute(ExpressionExperiment ee, PreparedCoexMatrices matrices)
Computes sample correlation matrices for the given experiment.DoubleMatrix<BioAssay,BioAssay>
SampleCoexpressionAnalysisService. compute(ExpressionExperiment ee, PreparedCoexMatrices matrices)
Computes sample correlation matrices for the given experiment.DoubleMatrix<BioAssay,BioAssay>
SampleCoexpressionAnalysisServiceImpl. compute(ExpressionExperiment ee, PreparedCoexMatrices matrices)
Unfortunately, this method breaks under high contention (see #400, so we need to fully lock the database while undergoing usingIsolation.SERIALIZABLE
transaction isolation level.DoubleMatrix<BioAssay,BioAssay>
SampleCoexpressionAnalysisServiceImpl. compute(ExpressionExperiment ee, PreparedCoexMatrices matrices)
Unfortunately, this method breaks under high contention (see #400, so we need to fully lock the database while undergoing usingIsolation.SERIALIZABLE
transaction isolation level.DoubleMatrix<BioAssay,BioAssay>
SampleCoexpressionAnalysisService. loadBestMatrix(ExpressionExperiment ee)
Loads the analysis containing the coexpression matrices for the given experiment and converts the regressed coexpression matrix into a double matrix.DoubleMatrix<BioAssay,BioAssay>
SampleCoexpressionAnalysisService. loadBestMatrix(ExpressionExperiment ee)
Loads the analysis containing the coexpression matrices for the given experiment and converts the regressed coexpression matrix into a double matrix.DoubleMatrix<BioAssay,BioAssay>
SampleCoexpressionAnalysisServiceImpl. loadBestMatrix(ExpressionExperiment ee)
DoubleMatrix<BioAssay,BioAssay>
SampleCoexpressionAnalysisServiceImpl. loadBestMatrix(ExpressionExperiment ee)
DoubleMatrix<BioAssay,BioAssay>
SampleCoexpressionAnalysisService. loadFullMatrix(ExpressionExperiment ee)
Loads the analysis containing the coexpression matrices for the given experiment and converts the full (non-regressed) coexpression matrix into a double matrix.DoubleMatrix<BioAssay,BioAssay>
SampleCoexpressionAnalysisService. loadFullMatrix(ExpressionExperiment ee)
Loads the analysis containing the coexpression matrices for the given experiment and converts the full (non-regressed) coexpression matrix into a double matrix.DoubleMatrix<BioAssay,BioAssay>
SampleCoexpressionAnalysisServiceImpl. loadFullMatrix(ExpressionExperiment ee)
DoubleMatrix<BioAssay,BioAssay>
SampleCoexpressionAnalysisServiceImpl. loadFullMatrix(ExpressionExperiment ee)
DoubleMatrix<BioAssay,BioAssay>
SampleCoexpressionAnalysisService. loadRegressedMatrix(ExpressionExperiment ee)
Load the regressed coexpression matrix for the given experiment.DoubleMatrix<BioAssay,BioAssay>
SampleCoexpressionAnalysisService. loadRegressedMatrix(ExpressionExperiment ee)
Load the regressed coexpression matrix for the given experiment.DoubleMatrix<BioAssay,BioAssay>
SampleCoexpressionAnalysisServiceImpl. loadRegressedMatrix(ExpressionExperiment ee)
DoubleMatrix<BioAssay,BioAssay>
SampleCoexpressionAnalysisServiceImpl. loadRegressedMatrix(ExpressionExperiment ee)
DoubleMatrix<BioAssay,BioAssay>
SampleCoexpressionAnalysisService. retrieveExisting(ExpressionExperiment ee)
DoubleMatrix<BioAssay,BioAssay>
SampleCoexpressionAnalysisService. retrieveExisting(ExpressionExperiment ee)
DoubleMatrix<BioAssay,BioAssay>
SampleCoexpressionAnalysisServiceImpl. retrieveExisting(ExpressionExperiment ee)
DoubleMatrix<BioAssay,BioAssay>
SampleCoexpressionAnalysisServiceImpl. retrieveExisting(ExpressionExperiment ee)
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Uses of BioAssay in ubic.gemma.persistence.service.expression.arrayDesign
Methods in ubic.gemma.persistence.service.expression.arrayDesign that return types with arguments of type BioAssay Modifier and Type Method Description Collection<BioAssay>
ArrayDesignDao. getAllAssociatedBioAssays(ArrayDesign arrayDesign)
Collection<BioAssay>
ArrayDesignDaoImpl. getAllAssociatedBioAssays(ArrayDesign arrayDesign)
Collection<BioAssay>
ArrayDesignService. getAllAssociatedBioAssays(ArrayDesign arrayDesign)
Collection<BioAssay>
ArrayDesignServiceImpl. getAllAssociatedBioAssays(ArrayDesign arrayDesign)
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Uses of BioAssay in ubic.gemma.persistence.service.expression.bioAssay
Methods in ubic.gemma.persistence.service.expression.bioAssay that return BioAssay Modifier and Type Method Description BioAssay
BioAssayService. create(BioAssay bioAssay)
BioAssay
BioAssayDaoImpl. find(BioAssay bioAssay)
BioAssay
BioAssayService. findOrCreate(BioAssay bioAssay)
BioAssay
BioAssayService. load(Long id)
BioAssay
BioAssayService. thaw(BioAssay bioAssay)
BioAssay
BioAssayServiceImpl. thaw(BioAssay bioAssay)
Methods in ubic.gemma.persistence.service.expression.bioAssay that return types with arguments of type BioAssay Modifier and Type Method Description Collection<BioAssay>
BioAssayDao. findByAccession(String accession)
Collection<BioAssay>
BioAssayDaoImpl. findByAccession(String accession)
Collection<BioAssay>
BioAssayService. findByAccession(String accession)
Collection<BioAssay>
BioAssayServiceImpl. findByAccession(String accession)
Collection<BioAssay>
BioAssayService. load(Collection<Long> ids)
Collection<BioAssay>
BioAssayService. loadAll()
Collection<BioAssay>
BioAssayService. thaw(Collection<BioAssay> bioAssays)
Collection<BioAssay>
BioAssayServiceImpl. thaw(Collection<BioAssay> bioAssays)
Methods in ubic.gemma.persistence.service.expression.bioAssay with parameters of type BioAssay Modifier and Type Method Description void
BioAssayService. addBioMaterialAssociation(BioAssay bioAssay, BioMaterial bioMaterial)
Associates a bioMaterial with a specified bioAssay.void
BioAssayServiceImpl. addBioMaterialAssociation(BioAssay bioAssay, BioMaterial bioMaterial)
BioAssay
BioAssayService. create(BioAssay bioAssay)
protected BioAssayValueObject
BioAssayDaoImpl. doLoadValueObject(BioAssay entity)
BioAssay
BioAssayDaoImpl. find(BioAssay bioAssay)
Collection<BioAssayDimension>
BioAssayDao. findBioAssayDimensions(BioAssay bioAssay)
Collection<BioAssayDimension>
BioAssayDaoImpl. findBioAssayDimensions(BioAssay bioAssay)
Collection<BioAssayDimension>
BioAssayService. findBioAssayDimensions(BioAssay bioAssay)
Locate all BioAssayDimensions in which the selected BioAssay occursCollection<BioAssayDimension>
BioAssayServiceImpl. findBioAssayDimensions(BioAssay bioAssay)
BioAssay
BioAssayService. findOrCreate(BioAssay bioAssay)
void
BioAssayService. remove(BioAssay bioAssay)
void
BioAssayService. removeBioMaterialAssociation(BioAssay bioAssay, BioMaterial bioMaterial)
Removes the association between a specific bioMaterial and a bioAssay.void
BioAssayServiceImpl. removeBioMaterialAssociation(BioAssay bioAssay, BioMaterial bioMaterial)
BioAssay
BioAssayService. thaw(BioAssay bioAssay)
BioAssay
BioAssayServiceImpl. thaw(BioAssay bioAssay)
void
BioAssayService. update(BioAssay bioAssay)
Method parameters in ubic.gemma.persistence.service.expression.bioAssay with type arguments of type BioAssay Modifier and Type Method Description List<BioAssayValueObject>
BioAssayDao. loadValueObjects(Collection<BioAssay> entities, Map<Long,ArrayDesignValueObject> arrayDesignValueObjects, boolean basic)
List<BioAssayValueObject>
BioAssayDaoImpl. loadValueObjects(Collection<BioAssay> entities, Map<Long,ArrayDesignValueObject> arrayDesignValueObjects, boolean basic)
Method that allows specification of FactorValueBasicValueObject in the bioMaterialVOsList<BioAssayValueObject>
BioAssayService. loadValueObjects(Collection<BioAssay> entities, boolean basic)
List<BioAssayValueObject>
BioAssayServiceImpl. loadValueObjects(Collection<BioAssay> entities, boolean basic)
Collection<BioAssay>
BioAssayService. thaw(Collection<BioAssay> bioAssays)
Collection<BioAssay>
BioAssayServiceImpl. thaw(Collection<BioAssay> bioAssays)
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Uses of BioAssay in ubic.gemma.persistence.service.expression.experiment
Methods in ubic.gemma.persistence.service.expression.experiment with parameters of type BioAssay Modifier and Type Method Description ExpressionExperiment
ExpressionExperimentDao. findByBioAssay(BioAssay ba)
ExpressionExperiment
ExpressionExperimentDaoImpl. findByBioAssay(BioAssay ba)
ExpressionExperiment
ExpressionExperimentService. findByBioAssay(BioAssay ba)
ExpressionExperiment
ExpressionExperimentServiceImpl. findByBioAssay(BioAssay ba)
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Uses of BioAssay in ubic.gemma.persistence.util
Methods in ubic.gemma.persistence.util with parameters of type BioAssay Modifier and Type Method Description static void
BusinessKey. addRestrictions(Criteria queryObject, BioAssay bioAssay)
static Criteria
BusinessKey. createQueryObject(Session session, BioAssay bioAssay)
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