Package ubic.gemma.core.datastructure.matrix

Class ExpressionDataDoubleMatrixUtil

java.lang.Object

ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrixUtil

public class ExpressionDataDoubleMatrixUtil
extends Object

Perform various computations on ExpressionDataMatrices (usually in-place).

Author:

pavlidis

Constructor Summary

Constructors

Constructor	Description
ExpressionDataDoubleMatrixUtil()

Method Summary

Modifier and Type	Method	Description
static void	addMatrices(ExpressionDataDoubleMatrix a, ExpressionDataDoubleMatrix b)	Add two matrices.
static void	detectSuspiciousValues(ExpressionDataDoubleMatrix a, QuantitationType qt)	Detect suspicious values for a given quantitation type.
static ExpressionDataDoubleMatrix	ensureLog2Scale(ExpressionDataDoubleMatrix expressionData)
static ExpressionDataDoubleMatrix	ensureLog2Scale(ExpressionDataDoubleMatrix dmatrix, boolean ignoreQuantitationMismatch)	Ensures that the given matrix is on a Log2 scale.
static ExpressionDataDoubleMatrix	filterAndLog2Transform(ExpressionDataDoubleMatrix dmatrix)	Log2 transform if necessary, do any required filtering prior to analysis.
static QuantitationType	inferQuantitationType(ExpressionDataDoubleMatrix expressionDataDoubleMatrix)	Infer a QuantitationType from expression data.
static void	logTransformMatrix(ExpressionDataDoubleMatrix matrix)	Log-transform the values in the matrix (base 2).
static void	maskMatrix(ExpressionDataDoubleMatrix matrix, ExpressionDataBooleanMatrix mask)	Use the mask matrix to turn some values in a matrix to NaN.
static void	scalarDivideMatrix(ExpressionDataDoubleMatrix matrix, double dividend)	Divide all values by the dividend
static void	subtractMatrices(ExpressionDataDoubleMatrix a, ExpressionDataDoubleMatrix b)	Subtract two matrices.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

ExpressionDataDoubleMatrixUtil

public ExpressionDataDoubleMatrixUtil()

Method Detail

filterAndLog2Transform

public static ExpressionDataDoubleMatrix filterAndLog2Transform(ExpressionDataDoubleMatrix dmatrix)

Log2 transform if necessary, do any required filtering prior to analysis. Count data is converted to log2CPM (but we store log2cpm as the processed data, so that is what would generally be used).

Parameters:

dmatrix - matrix

Returns:

ee data double matrix

ensureLog2Scale

@CheckReturnValue
public static ExpressionDataDoubleMatrix ensureLog2Scale(ExpressionDataDoubleMatrix dmatrix,
                                                         boolean ignoreQuantitationMismatch)
                                                  throws QuantitationMismatchException

Ensures that the given matrix is on a Log2 scale. ! Does not update the QT !

Parameters:

dmatrix - the matrix to be transformed to a log2 scale if necessary.

ignoreQuantitationMismatch - if true, ignore mismatch between matrix quantitation types and that inferred from data

Returns:

a data matrix that is guaranteed to be on a log2 scale or the original input matrix if it was already the case

Throws:

QuantitationTypeConversionException - if transformation to log2 scale is impossible

InferredQuantitationMismatchException - if the inferred scale type differs that inferred from data

QuantitationMismatchException

ensureLog2Scale

public static ExpressionDataDoubleMatrix ensureLog2Scale(ExpressionDataDoubleMatrix expressionData)

inferQuantitationType

public static QuantitationType inferQuantitationType(ExpressionDataDoubleMatrix expressionDataDoubleMatrix)

Infer a QuantitationType from expression data.

detectSuspiciousValues

public static void detectSuspiciousValues(ExpressionDataDoubleMatrix a,
                                          QuantitationType qt)
                                   throws SuspiciousValuesForQuantitationException

Detect suspicious values for a given quantitation type.

Throws:

SuspiciousValuesForQuantitationException - if there are any suspicious values

subtractMatrices

public static void subtractMatrices(ExpressionDataDoubleMatrix a,
                                    ExpressionDataDoubleMatrix b)

Subtract two matrices. Ideally, they matrices are conformant, but if they are not (as some rows are sometimes missing for some quantitation types), this method attempts to handle it anyway (see below). The rows and columns do not have to be in the same order, but they do have to have the same column keys and row keys (with the exception of missing rows). The result is stored in a. (a - b). If the number of rows are not the same, and/or the rows have different keys in the two matrices, some rows will simply not get subtracted and a warning will be issued.

Parameters:

a - matrix a

b - matrix b

Throws:

IllegalArgumentException - if the matrices are not column-conformant.

logTransformMatrix

public static void logTransformMatrix(ExpressionDataDoubleMatrix matrix)

Log-transform the values in the matrix (base 2). Non-positive values (which have no logarithm defined) are entered as NaN.

Parameters:

matrix - matrix

addMatrices

public static void addMatrices(ExpressionDataDoubleMatrix a,
                               ExpressionDataDoubleMatrix b)

Add two matrices. Ideally, they matrices are conformant, but if they are not (as some rows are sometimes missing for some quantitation types), this method attempts to handle it anyway (see below). The rows and columns do not have to be in the same order, but they do have to have the same column keys and row keys (with the exception of missing rows). The result is stored in a. If the number of rows are not the same, and/or the rows have different keys in the two matrices, some rows will simply not get added and a warning will be issued.

Parameters:

a - matrix a

b - matrix b

Throws:

IllegalArgumentException - if the matrices are not column-conformant.

scalarDivideMatrix

public static void scalarDivideMatrix(ExpressionDataDoubleMatrix matrix,
                                      double dividend)

Divide all values by the dividend

Parameters:

matrix - matrix

dividend - dividend

Throws:

IllegalArgumentException - if dividend == 0.

maskMatrix

public static void maskMatrix(ExpressionDataDoubleMatrix matrix,
                              ExpressionDataBooleanMatrix mask)

Use the mask matrix to turn some values in a matrix to NaN. Ideally, they matrices are conformant, but if they are not (as some rows are sometimes missing for some quantitation types), this method attempts to handle it anyway (see below). The rows and columns do not have to be in the same order, but they do have to have the same column keys and row keys (with the exception of missing rows). The result is stored in matrix.

Parameters:

matrix - matrix

mask - if null, masking is not attempted.