Uses of Interface
ubic.gemma.core.util.matrix.ObjectMatrix

Packages that use ObjectMatrix

Package	Description
ubic.gemma.core.analysis.expression.diff
ubic.gemma.core.util.math.linearmodels
ubic.gemma.core.util.matrix	Labelled-axis matrix types ported in-tree from baseCode's ubic.basecode.dataStructure.matrix subsystem as part of the Phase 3 baseCode retirement (see BASECODE_MATRIX_RECCE.md and BASECODE_DEP_AUDIT.md).

Uses of ObjectMatrix in ubic.gemma.core.analysis.expression.diff

Methods in ubic.gemma.core.analysis.expression.diff that return ObjectMatrix

Modifier and Type	Method	Description
static ObjectMatrix<BioMaterial, ExperimentalFactor, Object>	DiffExAnalyzerUtils.buildDesignMatrix(List<ExperimentalFactor> factors, List<BioMaterial> samplesUsed, boolean allowMissingValues)	Build a design matrix for the given factors and samples.
static ObjectMatrix<String,String,Object>	DiffExAnalyzerUtils.buildRDesignMatrix(List<ExperimentalFactor> factors, List<BioMaterial> samplesUsed, boolean allowMissingValues)	Build an R-friendly design matrix.
static ObjectMatrix<String,String,Object>	DiffExAnalyzerUtils.buildRDesignMatrix(List<ExperimentalFactor> factors, List<BioMaterial> samplesUsed, Map<ExperimentalFactor, FactorValue> baselines, boolean allowMissingValues)	A variant of DiffExAnalyzerUtils.buildRDesignMatrix(List, List, boolean) that allows for reusing baselines for repeated calls.

Methods in ubic.gemma.core.analysis.expression.diff with parameters of type ObjectMatrix

Modifier and Type	Method	Description
static DoubleMatrix<String,String>	DiffExAnalyzerUtils.makeDataMatrix(ObjectMatrix<String,String,Object> designMatrix, DoubleMatrix<CompositeSequence, BioMaterial> namedMatrix)	Convert the data into a string-keyed matrix.

Uses of ObjectMatrix in ubic.gemma.core.util.math.linearmodels

Methods in ubic.gemma.core.util.math.linearmodels with parameters of type ObjectMatrix

Modifier and Type	Method	Description
void	DesignMatrix.add(ObjectMatrix<String,String,Object> sampleInfo)	Append additional factors/covariates to this

Constructors in ubic.gemma.core.util.math.linearmodels with parameters of type ObjectMatrix

Modifier	Constructor	Description
	DesignMatrix(ObjectMatrix<String,String,?> sampleInfo, boolean intercept)
	DesignMatrix(ObjectMatrix<String, String, ? extends Object> sampleInfo)
	DesignMatrix(ObjectMatrix<String,String,Object> design, boolean intercept, boolean strict)
	LeastSquaresFit(ObjectMatrix<String,String,Object> sampleInfo, DenseDoubleMatrix2D data)
	LeastSquaresFit(ObjectMatrix<String,String,Object> sampleInfo, DenseDoubleMatrix2D data, boolean interactions)
	LeastSquaresFit(ObjectMatrix<String,String,Object> design, DoubleMatrix<String,String> b)	NamedMatrix allows easier handling of the results.
	LeastSquaresFit(ObjectMatrix<String,String,Object> design, DoubleMatrix<String,String> data, boolean interactions)	NamedMatrix allows easier handling of the results.

Uses of ObjectMatrix in ubic.gemma.core.util.matrix

Classes in ubic.gemma.core.util.matrix that implement ObjectMatrix

Modifier and Type	Class	Description
class	ObjectMatrixImpl<R,C,V>	Matrix that can hold any type of object
class	StringMatrix<R,C>	A NamedMatrix containing String objects.

Methods in ubic.gemma.core.util.matrix that return ObjectMatrix

Modifier and Type	Method	Description
ObjectMatrix<R,C,V>	ObjectMatrix.subset(int startRow, int startCol, int numRow, int numCol)
ObjectMatrix<R,C,V>	ObjectMatrixImpl.subset(int startRow, int startCol, int numRow, int numCol)
ObjectMatrix<R,C,String>	StringMatrix.subset(int startRow, int startCol, int numRow, int numCol)
ObjectMatrix<R,C,V>	ObjectMatrix.subsetColumns(List<C> columns)
ObjectMatrix<R,C,String>	StringMatrix.subsetColumns(List<C> columns)