Package ubic.gemma.model.expression.experiment

Class ExperimentalDesignUtils

java.lang.Object

ubic.gemma.model.expression.experiment.ExperimentalDesignUtils

public class ExperimentalDesignUtils
extends Object

Author:

paul

Field Summary

Fields

Modifier and Type	Field	Description
static String	BATCH_FACTOR_CATEGORY_NAME
static String	BATCH_FACTOR_CATEGORY_URI
static String	BATCH_FACTOR_NAME
static String	BATCH_FACTOR_NAME_PREFIX
static String	FACTOR_VALUE_RNAME_PREFIX

Constructor Summary

Constructors

Constructor	Description
ExperimentalDesignUtils()

Method Summary

Modifier and Type	Method	Description
static ObjectMatrix<String,String,Object>	buildDesignMatrix(List<ExperimentalFactor> factors, List<BioMaterial> samplesUsed, Map<ExperimentalFactor,FactorValue> baselines)	Convert factors to a matrix usable in R.
static Collection<ExperimentalFactor>	factorsWithoutBatch(Collection<ExperimentalFactor> factors)
static Map<ExperimentalFactor,FactorValue>	getBaselineConditions(List<BioMaterial> samplesUsed, List<ExperimentalFactor> factors)
static List<BioMaterial>	getOrderedSamples(ExpressionDataDoubleMatrix dmatrix, List<ExperimentalFactor> factors)	This puts the control samples up front if possible.
static boolean	isBatch(ExperimentalFactor ef)
static boolean	isBatch(ExperimentalFactorValueObject ef)
static boolean	isComplete(ExperimentalFactor factor, List<BioMaterial> samplesUsed, Map<ExperimentalFactor,FactorValue> baselines)	Check if a factor has missing values (samples that lack an assigned value)
static boolean	isContinuous(ExperimentalFactor ef)
static String	nameForR(ExperimentalFactor experimentalFactor)
static String	nameForR(FactorValue fv, boolean isBaseline)
static ObjectMatrix<BioMaterial,ExperimentalFactor,Object>	sampleInfoMatrix(List<ExperimentalFactor> factors, List<BioMaterial> samplesUsed, Map<ExperimentalFactor,FactorValue> baselines)
static List<ExperimentalFactor>	sortFactors(Collection<ExperimentalFactor> factors)	Sort factors in a consistent way.

Methods inherited from class java.lang.Object

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

Field Detail

BATCH_FACTOR_CATEGORY_NAME

public static final String BATCH_FACTOR_CATEGORY_NAME

See Also:

Constant Field Values

BATCH_FACTOR_CATEGORY_URI

public static final String BATCH_FACTOR_CATEGORY_URI

See Also:

Constant Field Values

BATCH_FACTOR_NAME

public static final String BATCH_FACTOR_NAME

See Also:

Constant Field Values

BATCH_FACTOR_NAME_PREFIX

public static final String BATCH_FACTOR_NAME_PREFIX

See Also:

Constant Field Values

FACTOR_VALUE_RNAME_PREFIX

public static final String FACTOR_VALUE_RNAME_PREFIX

See Also:

Constant Field Values

Constructor Detail

ExperimentalDesignUtils

public ExperimentalDesignUtils()

Method Detail

isComplete

public static boolean isComplete(ExperimentalFactor factor,
                                 List<BioMaterial> samplesUsed,
                                 Map<ExperimentalFactor,FactorValue> baselines)

Check if a factor has missing values (samples that lack an assigned value)

Parameters:

baselines - not really important for this

samplesUsed - the samples used

factor - the factor

Returns:

false if there are any missing values.

buildDesignMatrix

public static ObjectMatrix<String,String,Object> buildDesignMatrix(List<ExperimentalFactor> factors,
                                                                               List<BioMaterial> samplesUsed,
                                                                               Map<ExperimentalFactor,FactorValue> baselines)

Convert factors to a matrix usable in R. The rows are in the same order as the columns of our data matrix (defined by samplesUsed).

Parameters:

factors - in the order they will be used

samplesUsed - the samples used

baselines - the baselines

Returns:

a design matrix

factorsWithoutBatch

public static Collection<ExperimentalFactor> factorsWithoutBatch(Collection<ExperimentalFactor> factors)

Parameters:

factors - factors

Returns:

a new collection (same order as the input)

getBaselineConditions

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

getOrderedSamples

public static List<BioMaterial> getOrderedSamples(ExpressionDataDoubleMatrix dmatrix,
                                                  List<ExperimentalFactor> factors)

This puts the control samples up front if possible.

Parameters:

factors - factors

dmatrix - data matrix

Returns:

ordered samples

isBatch

public static boolean isBatch(ExperimentalFactor ef)

Parameters:

ef - experimental factor

Returns:

true if this factor appears to be a "batch" factor.

isBatch

public static boolean isBatch(ExperimentalFactorValueObject ef)

Parameters:

ef - experimental factor

Returns:

true if this factor appears to be a "batch" factor.

isContinuous

public static boolean isContinuous(ExperimentalFactor ef)

Parameters:

ef - experimental factor

Returns:

true if the factor is continuous; false if it looks to be categorical.

nameForR

public static String nameForR(ExperimentalFactor experimentalFactor)

nameForR

public static String nameForR(FactorValue fv,
                              boolean isBaseline)

sampleInfoMatrix

public static ObjectMatrix<BioMaterial,ExperimentalFactor,Object> sampleInfoMatrix(List<ExperimentalFactor> factors,
                                                                                               List<BioMaterial> samplesUsed,
                                                                                               Map<ExperimentalFactor,FactorValue> baselines)

Parameters:

factors - factors

baselines - baselines

samplesUsed - the samples used

Returns:

Experimental design matrix

sortFactors

public static List<ExperimentalFactor> sortFactors(Collection<ExperimentalFactor> factors)

Sort factors in a consistent way.

Parameters:

factors - factors

Returns:

sorted factors