Package ubic.gemma.core.datastructure.matrix

Interface MultiAssayBulkExpressionDataMatrix<T>

Type Parameters:

T -

All Superinterfaces:

BulkExpressionDataMatrix<T>, ExpressionDataMatrix<T>

All Known Implementing Classes:

AbstractMultiAssayExpressionDataMatrix, EmptyExpressionMatrix, ExpressionDataBooleanMatrix, ExpressionDataDoubleMatrix, ExpressionDataIntegerMatrix, ExpressionDataStringMatrix

public interface MultiAssayBulkExpressionDataMatrix<T>
extends BulkExpressionDataMatrix<T>

An interface for bulk matrices that supports multiple BioAssay per BioMaterial.

This is usually achieved by stacking data matrices from multiple QuantitationType.

Method Summary

Modifier and Type	Method	Description
int	columns(CompositeSequence el)	Number of columns that use the given design element.
Optional<BioAssayDimension>	getBestBioAssayDimension()	Obtain the largest BioAssayDimension that covers all the biomaterials in this matrix.
BioAssayDimension	getBioAssayDimension()	Obtain the dimension for the columns of this matrix.
BioAssayDimension	getBioAssayDimension(CompositeSequence designElement)	Produce a BioAssayDimension representing the matrix columns for a specific row.
Collection<BioAssayDimension>	getBioAssayDimensions()	Obtain all the BioAssayDimensions that are used in this matrix.
Collection<BioAssay>	getBioAssaysForColumn(int index)
BioMaterial	getBioMaterialForColumn(int index)	Obtain a biomaterial corresponding to a column.
int	getColumnIndex(BioMaterial bioMaterial)
static MultiAssayBulkExpressionDataMatrix<?>	getMatrix(Collection<? extends BulkExpressionDataVector> vectors)	Create a matrix using all the vectors, which are assumed to share the same representation.
QuantitationType	getQuantitationType()	Obtain the quantitation type for this matrix.
Collection<QuantitationType>	getQuantitationTypes()	Return the quantitation types for this matrix.

Methods inherited from interface ubic.gemma.core.datastructure.matrix.BulkExpressionDataMatrix

get, getBioAssayForColumn, getColumn, getColumnIndex, getRawMatrix, hasMissingValues

Methods inherited from interface ubic.gemma.core.datastructure.matrix.ExpressionDataMatrix

columns, get, getColumn, getDesignElementForRow, getDesignElements, getExpressionExperiment, getRow, getRow, getRowElement, getRowElements, getRowIndex, getRowIndices, rows, sliceRows

Method Details

getMatrix

static MultiAssayBulkExpressionDataMatrix<?> getMatrix(Collection<? extends BulkExpressionDataVector> vectors)

Create a matrix using all the vectors, which are assumed to share the same representation.

Parameters:

vectors - raw vectors

Returns:

matrix of appropriate type.

getQuantitationType

QuantitationType getQuantitationType()

Obtain the quantitation type for this matrix.

In the case of multi-assay matrices, more than one quantitation type may be present. When possible, those are merged with QuantitationTypeUtils.mergeQuantitationTypes(Collection).

Specified by:

getQuantitationType in interface ExpressionDataMatrix<T>

Throws:

IllegalStateException - if the matrix has more than one quantitation type that cannot be combined

getQuantitationTypes

Collection<QuantitationType> getQuantitationTypes()

Return the quantitation types for this matrix. Often (usually) there will be just one.

getBioAssayDimensions

Collection<BioAssayDimension> getBioAssayDimensions()

Obtain all the BioAssayDimensions that are used in this matrix.

getBioAssayDimension

BioAssayDimension getBioAssayDimension()

Obtain the dimension for the columns of this matrix.

Specified by:

getBioAssayDimension in interface BulkExpressionDataMatrix<T>

Throws:

IllegalStateException - if no BioAssayDimension covers all the biomaterials in this matrix

getBestBioAssayDimension

Optional<BioAssayDimension> getBestBioAssayDimension()

Obtain the largest BioAssayDimension that covers all the biomaterials in this matrix.

Returns:

the best BioAssayDimension for this matrix, or Optional.empty() if no such dimension exists

getBioAssayDimension

BioAssayDimension getBioAssayDimension(CompositeSequence designElement)

Produce a BioAssayDimension representing the matrix columns for a specific row. The designelement argument is needed because a matrix can combine data from multiple array designs, each of which will generate its own bioassaydimension. Note that if this represents a subsetted data set, the return value may be a lightweight 'fake'.

Parameters:

designElement - de

Returns:

bad

columns

int columns(CompositeSequence el)

Number of columns that use the given design element. Useful if the matrix includes data from more than one array design.

Parameters:

el - el

Returns:

int

getBioAssaysForColumn

Collection<BioAssay> getBioAssaysForColumn(int index)

Parameters:

index - i

Returns:

bioassays that contribute data to the column. There can be multiple bioassays if more than one array was used in the study.

getBioMaterialForColumn

BioMaterial getBioMaterialForColumn(int index)

Description copied from interface: BulkExpressionDataMatrix

Obtain a biomaterial corresponding to a column.

Specified by:

getBioMaterialForColumn in interface BulkExpressionDataMatrix<T>

Parameters:

index - i

Returns:

BioMaterial. Note that if this represents a subsetted data set, the BioMaterial may be a lightweight 'fake'.

getColumnIndex

int getColumnIndex(BioMaterial bioMaterial)

Specified by:

getColumnIndex in interface BulkExpressionDataMatrix<T>

Parameters:

bioMaterial - bm

Returns:

the index of the column for the data for the bioMaterial, or -1 if missing