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 List<BioMaterial>	orderByExperimentalDesign(List<BioMaterial> start, Collection<ExperimentalFactor> factors, ExperimentalFactor primaryFactor)
static <R> DoubleMatrix<R,BioAssay>	orderByExperimentalDesign(DoubleMatrix<R,BioAssay> mat, Collection<ExperimentalFactor> factors, ExperimentalFactor primaryFactor)
static List<BioMaterial>	orderByExperimentalDesign(BulkExpressionDataMatrix<?> dmatrix, Collection<ExperimentalFactor> factors, 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

orderByExperimentalDesign

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

orderByExperimentalDesign

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

orderByExperimentalDesign

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

Parameters:

start - biomaterials to sort

factors - factors to consider for ordering biomaterials or all of them if null

primaryFactor - first factor to consider when ordering, auto-detected if null

Returns:

sorted biomaterials