Uses of Interface
ubic.gemma.core.datastructure.matrix.ExpressionDataMatrix
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Packages that use ExpressionDataMatrix Package Description ubic.gemma.core.analysis.expression.diff ubic.gemma.core.analysis.preprocess ubic.gemma.core.datastructure.matrix -
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Uses of ExpressionDataMatrix in ubic.gemma.core.analysis.expression.diff
Methods in ubic.gemma.core.analysis.expression.diff with parameters of type ExpressionDataMatrix Modifier and Type Method Description static List<BioMaterial>
DifferentialExpressionAnalysisUtil. getBioMaterialsForBioAssays(ExpressionDataMatrix<?> matrix)
Returns a List of all the different types of biomaterials across all bioassays in the experiment. -
Uses of ExpressionDataMatrix in ubic.gemma.core.analysis.preprocess
Methods in ubic.gemma.core.analysis.preprocess that return ExpressionDataMatrix Modifier and Type Method Description static ExpressionDataMatrix<?>
ExpressionDataMatrixBuilder. getMatrix(Collection<? extends DesignElementDataVector> vectors)
Create a matrix using all the vectors, which are assumed to all be of the same quantitation type. -
Uses of ExpressionDataMatrix in ubic.gemma.core.datastructure.matrix
Classes in ubic.gemma.core.datastructure.matrix that implement ExpressionDataMatrix Modifier and Type Class Description class
BaseExpressionDataMatrix<T>
Base class for ExpressionDataMatrix implementations.class
EmptyExpressionMatrix
Used to make a 'dummy matrix' that has the column information populated.class
ExpressionDataBooleanMatrix
Matrix of booleans mapped from an ExpressionExperiment.class
ExpressionDataDoubleMatrix
A data structure that holds a reference to the data for a given expression experiment.class
ExpressionDataIntegerMatrix
Warning, not fully tested.class
ExpressionDataStringMatrix
Methods in ubic.gemma.core.datastructure.matrix with parameters of type ExpressionDataMatrix Modifier and Type Method Description static String
ExpressionDataWriterUtils. constructBioAssayName(ExpressionDataMatrix<?> matrix, int assayColumnIndex)
Constructs a bioassay name.static List<BioMaterial>
ExpressionDataMatrixColumnSort. orderByExperimentalDesign(ExpressionDataMatrix<?> mat)
static List<BioMaterial>
ExpressionDataMatrixColumnSort. orderByExperimentalDesign(ExpressionDataMatrix<?> mat, ExperimentalFactor primaryFactor)
void
MatrixWriter. write(Writer writer, ExpressionDataMatrix<?> matrix, Map<CompositeSequence,Collection<Gene>> geneAnnotations, boolean writeHeader, boolean orderByDesign)
void
MatrixWriter. write(Writer writer, ExpressionDataMatrix<?> matrix, Map<CompositeSequence,Collection<Gene>> geneAnnotations, boolean writeHeader, boolean writeSequence, boolean writeGeneInfo, boolean orderByDesign)
void
MatrixWriter. writeJSON(Writer writer, ExpressionDataMatrix<?> matrix)
void
MatrixWriter. writeTsv(ExpressionDataMatrix<?> entity, Writer writer)
void
MatrixWriter. writeWithStringifiedGeneAnnotations(Writer writer, ExpressionDataMatrix<?> matrix, Map<CompositeSequence,String[]> geneAnnotations, boolean writeHeader)
Alternate method that uses annotations in string form (e.g., read from another file).void
MatrixWriter. writeWithStringifiedGeneAnnotations(Writer writer, ExpressionDataMatrix<?> matrix, Map<CompositeSequence,String[]> geneAnnotations, boolean writeHeader, boolean writeSequence, boolean writeGeneInfo, boolean orderByDesign)
Constructors in ubic.gemma.core.datastructure.matrix with parameters of type ExpressionDataMatrix Constructor Description ExpressionDataMatrixRowElement(ExpressionDataMatrix<?> matrix, int i)
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