Package ubic.gemma.core.datastructure.matrix

Interface BulkExpressionDataMatrix<T>

All Superinterfaces:

ExpressionDataMatrix<T>

All Known Implementing Classes:

BaseExpressionDataMatrix, EmptyExpressionMatrix, ExpressionDataBooleanMatrix, ExpressionDataDoubleMatrix, ExpressionDataIntegerMatrix, ExpressionDataStringMatrix

public interface BulkExpressionDataMatrix<T>
extends ExpressionDataMatrix<T>

Interface for bulk expression data matrices.

In a bulk expression data matrix, each column represents a sample.

Expression data is rather complex, so we have to handle some messy cases.

The key problem is how to unambiguously identify rows and columns in the matrix. This is greatly complicated by the fact that experiments can combine data from multiple array designs in various ways.

Put it together, and the result is that there can be more than one BioAssay per column; the same BioMaterial can be used in multiple columns (supported implicitly). There can also be more than on BioMaterial in one column (we don't support this yet either). The same BioSequence can be found in multiple rows. A row can contain data from more than one CompositeSequence.

There are a few constraints: a particular CompositeSequence can only be used once, in a single row. At the moment we do not directly support technical replicates, though this should be possible. A BioAssay can only appear in a single column.

For some operations a ExpressionDataMatrixRowElement object is offered, which encapsulates a combination of CompositeSequence, a BioSequence, and an index. The list of these can be useful for iterating over the rows of the matrix.

Author:

pavlidis, keshav

See Also:

BioAssayDimension, BulkExpressionDataVector

Method Summary

Modifier and Type	Method	Description
int	columns(CompositeSequence el)	Number of columns that use the given design element.
T[][]	get(List<CompositeSequence> designElements, List<BioAssay> bioAssays)	Access a submatrix
T	get(CompositeSequence designElement, BioAssay bioAssay)	Access a single value of the matrix.
BioAssayDimension	getBestBioAssayDimension()
BioAssayDimension	getBioAssayDimension(CompositeSequence designElement)	Produce a BioAssayDimension representing the matrix columns for a specific row.
BioAssay	getBioAssayForColumn(int index)	Obtain a single assay for a column.
Collection<BioAssay>	getBioAssaysForColumn(int index)
BioMaterial	getBioMaterialForColumn(int index)
T[]	getColumn(BioAssay bioAssay)	Access a single column of the matrix.
int	getColumnIndex(BioAssay bioAssay)
int	getColumnIndex(BioMaterial bioMaterial)
T[][]	getColumns(List<BioAssay> bioAssays)	Access a submatrix slice by columns
ExpressionExperiment	getExpressionExperiment()	The experiment this matrix is associated with, if known.
static BulkExpressionDataMatrix<?>	getMatrix(Collection<? extends BulkExpressionDataVector> vectors)	Create a matrix using all the vectors, which are assumed to all be of the same quantitation type.
QuantitationType	getQuantitationType()	Obtain the single quantitation type for this matrix.
Collection<QuantitationType>	getQuantitationTypes()	Return the quantitation types for this matrix.
T[][]	getRawMatrix()	Access the entire matrix.
boolean	hasMissingValues()
void	set(int row, int column, T value)	Set a value in the matrix, by index

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

columns, get, getColumn, getDesignElementForRow, getDesignElements, getRow, getRow, getRowElement, getRowElement, getRowElements, getRowIndex, rows

Method Detail

getMatrix

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

Create a matrix using all the vectors, which are assumed to all be of the same quantitation type.

Parameters:

vectors - raw vectors

Returns:

matrix of appropriate type.

getExpressionExperiment

@Nullable
ExpressionExperiment getExpressionExperiment()

The experiment this matrix is associated with, if known.

Specified by:

getExpressionExperiment in interface ExpressionDataMatrix<T>

getQuantitationTypes

Collection<QuantitationType> getQuantitationTypes()

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

Returns:

qts

getQuantitationType

QuantitationType getQuantitationType()

Obtain the single quantitation type for this matrix.

Throws:

IllegalStateException - if there is more than one quantitation type.

getBestBioAssayDimension

BioAssayDimension getBestBioAssayDimension()

Returns:

a BioAssayDimension that covers all the biomaterials in this matrix.

Throws:

IllegalStateException - if there isn't a single bioassaydimension that encapsulates all the biomaterials used in the experiment.

hasMissingValues

boolean hasMissingValues()

Returns:

true if any values are null or NaN (for Doubles); all other values are considered non-missing.

get

T get(CompositeSequence designElement,
      BioAssay bioAssay)

Access a single value of the matrix. Note that because there can be multiple bioassays per column and multiple designelements per row, it is possible for this method to retrieve a data that does not come from the bioassay and/or designelement arguments.

Parameters:

designElement - de

bioAssay - ba

Returns:

T t

get

T[][] get(List<CompositeSequence> designElements,
          List<BioAssay> bioAssays)

Access a submatrix

Parameters:

designElements - de

bioAssays - bas

Returns:

T[][]

getRawMatrix

T[][] getRawMatrix()

Access the entire matrix.

Returns:

T[][]

getColumn

T[] getColumn(BioAssay bioAssay)

Access a single column of the matrix.

Parameters:

bioAssay - i

Returns:

T[]

getColumns

T[][] getColumns(List<BioAssay> bioAssays)

Access a submatrix slice by columns

Parameters:

bioAssays - ba

Returns:

t[][]

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

getBioMaterialForColumn

BioMaterial getBioMaterialForColumn(int index)

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)

Parameters:

bioMaterial - bm

Returns:

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

getColumnIndex

int getColumnIndex(BioAssay bioAssay)

Returns:

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

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

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.

getBioAssayForColumn

BioAssay getBioAssayForColumn(int index)

Obtain a single assay for a column.

Parameters:

index -

Returns:

Throws:

IllegalStateException - if there is more than one assay for the column.

set

void set(int row,
         int column,
         T value)

Set a value in the matrix, by index

Parameters:

row - row

column - col

value - val