Uses of Class
ubic.gemma.model.common.quantitationtype.QuantitationType
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Uses of QuantitationType in ubic.gemma.core.analysis.expression.coexpression.links
Methods in ubic.gemma.core.analysis.expression.coexpression.links that return QuantitationType Modifier and Type Method Description QuantitationType
LinkAnalysis. getMetric()
QuantitationType
MatrixRowPairAnalysis. getMetricType()
QuantitationType
PearsonMetrics. getMetricType()
QuantitationType
SpearmanMetrics. getMetricType()
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Uses of QuantitationType in ubic.gemma.core.analysis.expression.diff
Methods in ubic.gemma.core.analysis.expression.diff with parameters of type QuantitationType Modifier and Type Method Description ExperimentalFactor
DiffExAnalyzer. determineInterceptFactor(Collection<ExperimentalFactor> factors, QuantitationType quantitationType)
ExperimentalFactor
LinearModelAnalyzer. determineInterceptFactor(Collection<ExperimentalFactor> factors, QuantitationType quantitationType)
Determine if any factor should be treated as the intercept term. -
Uses of QuantitationType in ubic.gemma.core.analysis.preprocess
Methods in ubic.gemma.core.analysis.preprocess that return types with arguments of type QuantitationType Modifier and Type Method Description static Collection<QuantitationType>
ExpressionDataMatrixBuilder. getMissingValueQuantitationTypes(ExpressionExperiment expressionExperiment)
static Collection<QuantitationType>
ExpressionDataMatrixBuilder. getPreferredAndMissingQuantitationTypes(ExpressionExperiment expressionExperiment)
List<QuantitationType>
ExpressionDataMatrixBuilder. getPreferredQTypes()
static Collection<QuantitationType>
ExpressionDataMatrixBuilder. getPreferredQuantitationTypes(ExpressionExperiment expressionExperiment)
static Collection<QuantitationType>
ExpressionDataMatrixBuilder. getUsefulQuantitationTypes(Collection<QuantitationType> eeQtTypes)
static Collection<QuantitationType>
ExpressionDataMatrixBuilder. getUsefulQuantitationTypes(ExpressionExperiment expressionExperiment)
Methods in ubic.gemma.core.analysis.preprocess with parameters of type QuantitationType Modifier and Type Method Description Integer
ExpressionDataMatrixBuilder. getNumMissingValues(QuantitationType qt)
Method parameters in ubic.gemma.core.analysis.preprocess with type arguments of type QuantitationType Modifier and Type Method Description static Collection<QuantitationType>
ExpressionDataMatrixBuilder. getUsefulQuantitationTypes(Collection<QuantitationType> eeQtTypes)
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Uses of QuantitationType in ubic.gemma.core.analysis.service
Methods in ubic.gemma.core.analysis.service with parameters of type QuantitationType Modifier and Type Method Description ExpressionDataDoubleMatrix
ExpressionDataMatrixService. getRawExpressionDataMatrix(ExpressionExperiment ee, QuantitationType quantitationType)
Obtain a raw expression data matrix for a given quantitation typeExpressionDataDoubleMatrix
ExpressionDataMatrixServiceImpl. getRawExpressionDataMatrix(ExpressionExperiment ee, QuantitationType quantitationType)
File
ExpressionDataFileService. writeOrLocateJSONRawExpressionDataFile(ExpressionExperiment ee, QuantitationType type, boolean forceWrite)
File
ExpressionDataFileServiceImpl. writeOrLocateJSONRawExpressionDataFile(ExpressionExperiment ee, QuantitationType type, boolean forceWrite)
File
ExpressionDataFileService. writeOrLocateRawExpressionDataFile(ExpressionExperiment ee, QuantitationType type, boolean forceWrite)
Locate or create a new data file for the given quantitation type.File
ExpressionDataFileServiceImpl. writeOrLocateRawExpressionDataFile(ExpressionExperiment ee, QuantitationType type, boolean forceWrite)
void
ExpressionDataFileService. writeRawExpressionData(ExpressionExperiment ee, QuantitationType qt, Writer writer)
Write raw expression data to a given writer for a given quantitation type.void
ExpressionDataFileServiceImpl. writeRawExpressionData(ExpressionExperiment ee, QuantitationType qt, Writer writer)
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Uses of QuantitationType in ubic.gemma.core.datastructure.matrix
Methods in ubic.gemma.core.datastructure.matrix that return QuantitationType Modifier and Type Method Description QuantitationType
InferredQuantitationMismatchException. getInferredQuantitationType()
QuantitationType
QuantitationMismatchException. getQuantitationType()
Quantitation type for the data.static QuantitationType
ExpressionDataDoubleMatrixUtil. inferQuantitationType(ExpressionDataDoubleMatrix expressionDataDoubleMatrix)
Infer aQuantitationType
from expression data.Methods in ubic.gemma.core.datastructure.matrix that return types with arguments of type QuantitationType Modifier and Type Method Description Collection<QuantitationType>
BaseExpressionDataMatrix. getQuantitationTypes()
Collection<QuantitationType>
ExpressionDataMatrix. getQuantitationTypes()
Return the quantitation types for this matrix.Methods in ubic.gemma.core.datastructure.matrix with parameters of type QuantitationType Modifier and Type Method Description static void
ExpressionDataDoubleMatrixUtil. detectSuspiciousValues(ExpressionDataDoubleMatrix a, QuantitationType qt)
Detect suspicious values for a given quantitation type.Constructor parameters in ubic.gemma.core.datastructure.matrix with type arguments of type QuantitationType Constructor Description ExpressionDataBooleanMatrix(Collection<? extends DesignElementDataVector> vectors, List<QuantitationType> qtypes)
ExpressionDataDoubleMatrix(ExpressionDataDoubleMatrix sourceMatrix, DoubleMatrix<CompositeSequence,BioMaterial> dataMatrix, Collection<QuantitationType> quantitationTypes)
Create a data matrix like sourceMatrix but use the values and quantitations from dataMatrix. -
Uses of QuantitationType in ubic.gemma.core.loader.expression
Methods in ubic.gemma.core.loader.expression with parameters of type QuantitationType Modifier and Type Method Description void
DataUpdater. log2cpmFromCounts(ExpressionExperiment ee, QuantitationType qt)
void
DataUpdaterImpl. log2cpmFromCounts(ExpressionExperiment ee, QuantitationType qt)
RNA-seq: For back filling log2cpm when only counts are available.void
DataUpdater. replaceData(ExpressionExperiment ee, ArrayDesign targetPlatform, QuantitationType qt, DoubleMatrix<String,String> data)
void
DataUpdaterImpl. replaceData(ExpressionExperiment ee, ArrayDesign targetPlatform, QuantitationType qt, DoubleMatrix<String,String> data)
Replace the data associated with the experiment (or add it if there is none). -
Uses of QuantitationType in ubic.gemma.core.loader.expression.geo
Methods in ubic.gemma.core.loader.expression.geo with parameters of type QuantitationType Modifier and Type Method Description byte[]
GeoConverter. convertData(List<Object> vector, QuantitationType qt)
byte[]
GeoConverterImpl. convertData(List<Object> vector, QuantitationType qt)
Convert a vector of strings into a byte[] for saving in the database.static void
QuantitationTypeParameterGuesser. guessQuantitationTypeParameters(QuantitationType qt, String name, String description)
static void
QuantitationTypeParameterGuesser. guessQuantitationTypeParameters(QuantitationType qt, String name, String description, Object exampleValue)
Attempt to fill in the details of the quantitation type.protected static boolean
QuantitationTypeParameterGuesser. isPreferred(QuantitationType qt)
Determine if a quantitation type is 'preferred'. -
Uses of QuantitationType in ubic.gemma.model.association.phenotype
Methods in ubic.gemma.model.association.phenotype that return QuantitationType Modifier and Type Method Description QuantitationType
PhenotypeAssociation. getScoreType()
Deprecated.Methods in ubic.gemma.model.association.phenotype with parameters of type QuantitationType Modifier and Type Method Description void
PhenotypeAssociation. setScoreType(QuantitationType scoreType)
Deprecated. -
Uses of QuantitationType in ubic.gemma.model.common.quantitationtype
Methods in ubic.gemma.model.common.quantitationtype that return QuantitationType Modifier and Type Method Description static QuantitationType
QuantitationType.Factory. newInstance()
static QuantitationType
QuantitationType.Factory. newInstance(QuantitationType quantitationType)
Create a new QT with the same spec as the provided one.Methods in ubic.gemma.model.common.quantitationtype with parameters of type QuantitationType Modifier and Type Method Description static QuantitationType
QuantitationType.Factory. newInstance(QuantitationType quantitationType)
Create a new QT with the same spec as the provided one.Constructors in ubic.gemma.model.common.quantitationtype with parameters of type QuantitationType Constructor Description QuantitationTypeValueObject(QuantitationType qt)
QuantitationTypeValueObject(QuantitationType qt, ExpressionExperiment expressionExperiment, Class<? extends DesignElementDataVector> vectorType)
Create aQuantitationType
VO in the context of an associated experiment. -
Uses of QuantitationType in ubic.gemma.model.expression.bioAssayData
Methods in ubic.gemma.model.expression.bioAssayData that return QuantitationType Modifier and Type Method Description QuantitationType
DataVector. getQuantitationType()
Methods in ubic.gemma.model.expression.bioAssayData with parameters of type QuantitationType Modifier and Type Method Description void
DataVector. setQuantitationType(QuantitationType quantitationType)
DesignElementDataVector
DoubleVectorValueObject. toDesignElementDataVector(ExpressionExperiment ee, CompositeSequence cs, QuantitationType updatedQuantitationType)
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Uses of QuantitationType in ubic.gemma.model.expression.experiment
Methods in ubic.gemma.model.expression.experiment that return types with arguments of type QuantitationType Modifier and Type Method Description Set<QuantitationType>
ExpressionExperiment. getQuantitationTypes()
Method parameters in ubic.gemma.model.expression.experiment with type arguments of type QuantitationType Modifier and Type Method Description void
ExpressionExperiment. setQuantitationTypes(Set<QuantitationType> quantitationTypes)
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Uses of QuantitationType in ubic.gemma.persistence.persister
Methods in ubic.gemma.persistence.persister that return QuantitationType Modifier and Type Method Description protected QuantitationType
CommonPersister. persistQuantitationType(QuantitationType qType, AbstractPersister.Caches caches)
Methods in ubic.gemma.persistence.persister with parameters of type QuantitationType Modifier and Type Method Description protected QuantitationType
CommonPersister. persistQuantitationType(QuantitationType qType, AbstractPersister.Caches caches)
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Uses of QuantitationType in ubic.gemma.persistence.service.common.quantitationtype
Methods in ubic.gemma.persistence.service.common.quantitationtype that return QuantitationType Modifier and Type Method Description QuantitationType
QuantitationTypeService. create(QuantitationType quantitationType)
QuantitationType
QuantitationTypeDao. find(ExpressionExperiment ee, QuantitationType quantitationType)
Locate a QT associated with the given ee matching the specification of the passed quantitationType, or null if there isn't one.QuantitationType
QuantitationTypeDaoImpl. find(QuantitationType quantitationType)
QuantitationType
QuantitationTypeDaoImpl. find(ExpressionExperiment ee, QuantitationType quantitationType)
QuantitationType
QuantitationTypeService. find(ExpressionExperiment ee, QuantitationType quantitationType)
Locate a QT associated with the given ee matching the specification of the passed quantitationType, or null if there isn't one.QuantitationType
QuantitationTypeServiceImpl. find(ExpressionExperiment ee, QuantitationType quantitationType)
QuantitationType
QuantitationTypeService. findOrCreate(QuantitationType quantitationType)
Methods in ubic.gemma.persistence.service.common.quantitationtype that return types with arguments of type QuantitationType Modifier and Type Method Description List<QuantitationType>
QuantitationTypeDao. loadByDescription(String description)
List<QuantitationType>
QuantitationTypeDaoImpl. loadByDescription(String description)
List<QuantitationType>
QuantitationTypeService. loadByDescription(String description)
List<QuantitationType>
QuantitationTypeServiceImpl. loadByDescription(String description)
Methods in ubic.gemma.persistence.service.common.quantitationtype with parameters of type QuantitationType Modifier and Type Method Description QuantitationType
QuantitationTypeService. create(QuantitationType quantitationType)
protected QuantitationTypeValueObject
QuantitationTypeDaoImpl. doLoadValueObject(QuantitationType entity)
boolean
QuantitationTypeDao. existsByExpressionExperimentAndVectorType(QuantitationType quantitationType, ExpressionExperiment ee, Class<? extends DesignElementDataVector> dataVectorClass)
Test if a given quantitation type is used by a given experiment for a given vector type.boolean
QuantitationTypeDaoImpl. existsByExpressionExperimentAndVectorType(QuantitationType quantitationType, ExpressionExperiment ee, Class<? extends DesignElementDataVector> dataVectorClass)
boolean
QuantitationTypeService. existsByExpressionExperimentAndVectorType(QuantitationType quantitationType, ExpressionExperiment ee, Class<? extends DesignElementDataVector> dataVectorType)
Find a quantitation type by ID and vector type.boolean
QuantitationTypeServiceImpl. existsByExpressionExperimentAndVectorType(QuantitationType quantitationType, ExpressionExperiment ee, Class<? extends DesignElementDataVector> dataVectorType)
QuantitationType
QuantitationTypeDao. find(ExpressionExperiment ee, QuantitationType quantitationType)
Locate a QT associated with the given ee matching the specification of the passed quantitationType, or null if there isn't one.QuantitationType
QuantitationTypeDaoImpl. find(QuantitationType quantitationType)
QuantitationType
QuantitationTypeDaoImpl. find(ExpressionExperiment ee, QuantitationType quantitationType)
QuantitationType
QuantitationTypeService. find(ExpressionExperiment ee, QuantitationType quantitationType)
Locate a QT associated with the given ee matching the specification of the passed quantitationType, or null if there isn't one.QuantitationType
QuantitationTypeServiceImpl. find(ExpressionExperiment ee, QuantitationType quantitationType)
QuantitationType
QuantitationTypeService. findOrCreate(QuantitationType quantitationType)
void
QuantitationTypeService. remove(QuantitationType quantitationType)
void
QuantitationTypeService. update(QuantitationType quantitationType)
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Uses of QuantitationType in ubic.gemma.persistence.service.expression.bioAssayData
Method parameters in ubic.gemma.persistence.service.expression.bioAssayData with type arguments of type QuantitationType Modifier and Type Method Description Collection<T>
AbstractDesignElementDataVectorDao. find(Collection<QuantitationType> quantitationTypes)
Collection<T>
AbstractDesignElementDataVectorService. find(Collection<QuantitationType> quantitationTypes)
Collection<T>
DesignElementDataVectorDao. find(Collection<QuantitationType> quantitationTypes)
Collection<T>
AbstractDesignElementDataVectorService. findAndThaw(Collection<QuantitationType> quantitationTypes)
Collection<DesignElementDataVector>
RawAndProcessedExpressionDataVectorServiceImpl. findAndThaw(Collection<QuantitationType> quantitationTypes)
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Uses of QuantitationType in ubic.gemma.persistence.service.expression.experiment
Methods in ubic.gemma.persistence.service.expression.experiment that return QuantitationType Modifier and Type Method Description QuantitationType
ExpressionExperimentDao. getPreferredQuantitationType(ExpressionExperiment ee)
Obtain the preferred quantitation type, if available.QuantitationType
ExpressionExperimentDaoImpl. getPreferredQuantitationType(ExpressionExperiment ee)
QuantitationType
ExpressionExperimentService. getPreferredQuantitationType(ExpressionExperiment ee)
Iterates over the quantitation types for a given expression experiment and returns the preferred quantitation types.QuantitationType
ExpressionExperimentServiceImpl. getPreferredQuantitationType(ExpressionExperiment ee)
Methods in ubic.gemma.persistence.service.expression.experiment with parameters of type QuantitationType Modifier and Type Method Description ExpressionExperiment
ExpressionExperimentDao. findByQuantitationType(QuantitationType quantitationType)
ExpressionExperiment
ExpressionExperimentDaoImpl. findByQuantitationType(QuantitationType quantitationType)
ExpressionExperiment
ExpressionExperimentService. findByQuantitationType(QuantitationType type)
ExpressionExperiment
ExpressionExperimentServiceImpl. findByQuantitationType(QuantitationType type)
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Uses of QuantitationType in ubic.gemma.persistence.util
Methods in ubic.gemma.persistence.util with parameters of type QuantitationType Modifier and Type Method Description static void
BusinessKey. addRestrictions(Criteria queryObject, QuantitationType quantitationType)
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Uses of QuantitationType in ubic.gemma.rest.util.args
Methods in ubic.gemma.rest.util.args that return QuantitationType Modifier and Type Method Description QuantitationType
QuantitationTypeArgService. getEntity(QuantitationTypeArg<?> quantitationTypeArg, ExpressionExperiment ee, Class<? extends DesignElementDataVector> vectorType)
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Uses of QuantitationType in ubic.gemma.web.controller.visualization
Methods in ubic.gemma.web.controller.visualization that return QuantitationType Modifier and Type Method Description QuantitationType
ExpressionExperimentVisualizationCommand. getQuantitationType()
Methods in ubic.gemma.web.controller.visualization with parameters of type QuantitationType Modifier and Type Method Description void
ExpressionExperimentVisualizationCommand. setQuantitationType(QuantitationType quantitationType)
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Uses of QuantitationType in ubic.gemma.web.propertyeditor
Constructor parameters in ubic.gemma.web.propertyeditor with type arguments of type QuantitationType Constructor Description QuantitationTypePropertyEditor(Collection<QuantitationType> types)
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