Package ubic.gemma.core.datastructure.matrix

Class ExpressionDataMatrixColumnSort

java.lang.Object

ubic.gemma.core.datastructure.matrix.ExpressionDataMatrixColumnSort

public class ExpressionDataMatrixColumnSort
extends Object

Methods to organize ExpressionDataMatrices by column (or at least provide the ordering). This works by greedily finding the factor with the fewest categories, sorting the samples by the factor values (measurements are treated as numbers if possible), and recursively repeating this for each block, until there are no more factors with more than one value.

Author:

paul

Constructor Summary

Constructors

Constructor	Description
ExpressionDataMatrixColumnSort()

Method Summary

Modifier and Type	Method	Description
static Map<ExperimentalFactor,FactorValue>	getBaselineLevels(Collection<ExperimentalFactor> factors)	Identify the FactorValue that should be treated as 'Baseline' for each of the given factors.
static Map<ExperimentalFactor,FactorValue>	getBaselineLevels(List<BioMaterial> samplesUsed, Collection<ExperimentalFactor> factors)	Identify the FactorValue that should be treated as 'Baseline' for each of the given factors.
static List<BioMaterial>	orderByExperimentalDesign(List<BioMaterial> start, Collection<ExperimentalFactor> factors)
static List<BioMaterial>	orderByExperimentalDesign(List<BioMaterial> start, Collection<ExperimentalFactor> factors, ExperimentalFactor primaryFactor)
static <R> DoubleMatrix<R,BioAssay>	orderByExperimentalDesign(DoubleMatrix<R,BioAssay> mat)
static <R> DoubleMatrix<R,BioAssay>	orderByExperimentalDesign(DoubleMatrix<R,BioAssay> mat, ExperimentalFactor primaryFactor)
static List<BioMaterial>	orderByExperimentalDesign(ExpressionDataMatrix<?> mat)
static List<BioMaterial>	orderByExperimentalDesign(ExpressionDataMatrix<?> mat, ExperimentalFactor primaryFactor)

Methods inherited from class java.lang.Object

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

Constructor Detail

ExpressionDataMatrixColumnSort

public ExpressionDataMatrixColumnSort()

Method Detail

getBaselineLevels

public static Map<ExperimentalFactor,FactorValue> getBaselineLevels(Collection<ExperimentalFactor> factors)

Identify the FactorValue that should be treated as 'Baseline' for each of the given factors. This is done heuristically, and if all else fails we choose arbitrarily.

Parameters:

factors - factors

Returns:

map

getBaselineLevels

public static Map<ExperimentalFactor,FactorValue> getBaselineLevels(List<BioMaterial> samplesUsed,
                                                                          Collection<ExperimentalFactor> factors)

Identify the FactorValue that should be treated as 'Baseline' for each of the given factors. This is done heuristically, and if all else fails we choose arbitrarily. For continuous factors, the minimum value is treated as baseline.

Parameters:

samplesUsed - These are used to make sure we don't bother using factor values as baselines if they are not used by any of the samples. This is important for subsets. If null, this is ignored.

factors - factors

Returns:

map of factors to the baseline factorvalue for that factor.

orderByExperimentalDesign

public static <R> DoubleMatrix<R,BioAssay> orderByExperimentalDesign(DoubleMatrix<R,BioAssay> mat)

orderByExperimentalDesign

public static <R> DoubleMatrix<R,BioAssay> orderByExperimentalDesign(DoubleMatrix<R,BioAssay> mat,
                                                                           @Nullable
                                                                           ExperimentalFactor primaryFactor)

orderByExperimentalDesign

public static List<BioMaterial> orderByExperimentalDesign(ExpressionDataMatrix<?> mat)

orderByExperimentalDesign

public static List<BioMaterial> orderByExperimentalDesign(ExpressionDataMatrix<?> mat,
                                                          @Nullable
                                                          ExperimentalFactor primaryFactor)

Parameters:

mat - matrix

Returns:

bio materials

orderByExperimentalDesign

public static List<BioMaterial> orderByExperimentalDesign(List<BioMaterial> start,
                                                          Collection<ExperimentalFactor> factors)

Parameters:

start - BioMaterials to sort

Returns:

bio materials

orderByExperimentalDesign

public static List<BioMaterial> orderByExperimentalDesign(List<BioMaterial> start,
                                                          @Nullable
                                                          Collection<ExperimentalFactor> factors,
                                                          @Nullable
                                                          ExperimentalFactor primaryFactor)

Parameters:

start - BioMaterials to sort

factors - , can be null

primaryFactor - to start with, can be null

Returns:

bio materials