Package ubic.gemma.core.analysis.expression.diff

Class DiffExAnalyzerUtils

java.lang.Object

ubic.gemma.core.analysis.expression.diff.DiffExAnalyzerUtils

public class DiffExAnalyzerUtils
extends Object

Constructor Summary

Constructors

Constructor	Description
DiffExAnalyzerUtils()

Method Summary

Modifier and Type	Method	Description
static BioAssayDimension	createBADMap(List<BioMaterial> columnsToUse)	This bioAssayDimension shouldn't get persisted; it is only for dealing with subset diff ex. analyses.
static AnalysisType	determineAnalysisType(BioAssaySet bioAssaySet, Collection<ExperimentalFactor> experimentalFactors, ExperimentalFactor subsetFactor, boolean includeInteractionsIfPossible)	Determines the analysis to execute based on the experimental factors, factor values, and block design.
static AnalysisType	determineAnalysisType(BioAssaySet bioAssaySet, DifferentialExpressionAnalysisConfig config)	FIXME this should probably deal with the case of outliers and also the LinearModelAnalyzer's EXCLUDE_CHARACTERISTICS_VALUES
static DoubleMatrix<String,String>	makeDataMatrix(ObjectMatrix<String,String,Object> designMatrix, DoubleMatrix<CompositeSequence,BioMaterial> namedMatrix)	Convert the data into a string-keyed matrix.
static String	nameForR(CompositeSequence cs)
static void	populateFactorValuesFromBASet(BioAssaySet ee, ExperimentalFactor f, Collection<FactorValue> fvs)
static void	writeConfig(DifferentialExpressionAnalysisConfig config, Writer writer)

Methods inherited from class java.lang.Object

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

Constructor Detail

DiffExAnalyzerUtils

public DiffExAnalyzerUtils()

Method Detail

createBADMap

public static BioAssayDimension createBADMap(List<BioMaterial> columnsToUse)

This bioAssayDimension shouldn't get persisted; it is only for dealing with subset diff ex. analyses.

Parameters:

columnsToUse - columns to use

Returns:

bio assay dimension

populateFactorValuesFromBASet

public static void populateFactorValuesFromBASet(BioAssaySet ee,
                                                 ExperimentalFactor f,
                                                 Collection<FactorValue> fvs)

makeDataMatrix

public static DoubleMatrix<String,String> makeDataMatrix(ObjectMatrix<String,String,Object> designMatrix,
                                                               DoubleMatrix<CompositeSequence,BioMaterial> namedMatrix)

Convert the data into a string-keyed matrix. Assumes that the row names of the designMatrix are concordant with the column names of the namedMatrix

nameForR

public static String nameForR(CompositeSequence cs)

determineAnalysisType

public static AnalysisType determineAnalysisType(BioAssaySet bioAssaySet,
                                                 DifferentialExpressionAnalysisConfig config)

FIXME this should probably deal with the case of outliers and also the LinearModelAnalyzer's EXCLUDE_CHARACTERISTICS_VALUES

Returns:

selected type of analysis such as t-test, two-way ANOVA, etc.

determineAnalysisType

public static AnalysisType determineAnalysisType(BioAssaySet bioAssaySet,
                                                 Collection<ExperimentalFactor> experimentalFactors,
                                                 @Nullable
                                                 ExperimentalFactor subsetFactor,
                                                 boolean includeInteractionsIfPossible)

Determines the analysis to execute based on the experimental factors, factor values, and block design.

FIXME: this should probably deal with the case of outliers and also the LinearModelAnalyzer's EXCLUDE_CHARACTERISTICS_VALUES

Parameters:

bioAssaySet - experiment or subset to determine the analysis type for

experimentalFactors - which factors to use, or null if to use all from the experiment

subsetFactor - can be null

includeInteractionsIfPossible - include interactions among the provided experimental factors if possible

Returns:

an appropriate analysis type

writeConfig

public static void writeConfig(DifferentialExpressionAnalysisConfig config,
                               Writer writer)
                        throws IOException

Throws:

IOException