Package ubic.gemma.model.expression.experiment

Class ExperimentalDesignUtils

java.lang.Object

ubic.gemma.model.expression.experiment.ExperimentalDesignUtils

@ParametersAreNonnullByDefault
public class ExperimentalDesignUtils
extends Object

Author:

paul

Field Summary

Fields

Modifier and Type	Field	Description
static List<Category>	BATCH_FACTOR_CATEGORIES	A list of all categories considered to be batch.
static String	BATCH_FACTOR_NAME	Name used by a batch factor.
static String	BIO_MATERIAL_RNAME_PREFIX
static String	FACTOR_RNAME_PREFIX
static String	FACTOR_VALUE_BASELINE_SUFFIX
static String	FACTOR_VALUE_RNAME_PREFIX

Constructor Summary

Constructors

Constructor	Description
ExperimentalDesignUtils()

Method Summary

Modifier and Type	Method	Description
static ObjectMatrix<BioMaterial,ExperimentalFactor,Object>	buildDesignMatrix(List<ExperimentalFactor> factors, List<BioMaterial> samplesUsed, boolean allowMissingValues)	Build a design matrix for the given factors and samples.
static ObjectMatrix<String,String,Object>	buildRDesignMatrix(List<ExperimentalFactor> factors, List<BioMaterial> samplesUsed, boolean allowMissingValues)	Build an R-friendly design matrix.
static ObjectMatrix<String,String,Object>	buildRDesignMatrix(List<ExperimentalFactor> factors, List<BioMaterial> samplesUsed, Map<ExperimentalFactor,FactorValue> baselines, boolean allowMissingValues)	A variant of buildRDesignMatrix(List, List, boolean) that allows for reusing baselines for repeated calls.
static Map<ExperimentalFactor,FactorValue>	getBaselineConditions(List<BioMaterial> samplesUsed, List<ExperimentalFactor> factors)
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(Collection<ExperimentalFactor> factors, List<BioMaterial> samplesUsed)	Identify the FactorValue that should be treated as 'Baseline' for each of the given factors.
static List<ExperimentalFactor>	getOrderedFactors(Collection<ExperimentalFactor> factors)	Sort factors in a consistent way.
static Map<BioMaterial,Set<FactorValue>>	getSampleToFactorValuesMap(ExperimentalFactor factor, Collection<BioMaterial> samplesUsed)	Create a sample to factor value mapping.
static boolean	isBatchFactor(ExperimentalFactor ef)	Check if a factor is a batch factor.
static boolean	isBatchFactor(ExperimentalFactorValueObject ef)	Check if a given factor VO is a batch factor.
static boolean	isComplete(ExperimentalFactor factor, List<BioMaterial> samplesUsed)	Check if a factor has missing values (samples that lack an assigned value)
static double	measurement2double(Measurement measurement)	Convert a measurement to a double.
static String	nameForR(BioMaterial sample)	Create a name for a sample suitable for R.
static String	nameForR(ExperimentalFactor experimentalFactor)	Create a name for the factor that is suitable for R.
static String	nameForR(FactorValue fv, boolean isBaseline)	Create a name for the factor value that is suitable for R.

Methods inherited from class java.lang.Object

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

Field Detail

BATCH_FACTOR_CATEGORIES

public static final List<Category> BATCH_FACTOR_CATEGORIES

A list of all categories considered to be batch.

BATCH_FACTOR_NAME

public static final String BATCH_FACTOR_NAME

Name used by a batch factor.

This is used only if the factor lacks a category.

See Also:

Constant Field Values

BIO_MATERIAL_RNAME_PREFIX

public static final String BIO_MATERIAL_RNAME_PREFIX

See Also:

Constant Field Values

FACTOR_RNAME_PREFIX

public static final String FACTOR_RNAME_PREFIX

See Also:

Constant Field Values

FACTOR_VALUE_RNAME_PREFIX

public static final String FACTOR_VALUE_RNAME_PREFIX

See Also:

Constant Field Values

FACTOR_VALUE_BASELINE_SUFFIX

public static final String FACTOR_VALUE_BASELINE_SUFFIX

See Also:

Constant Field Values

Constructor Detail

ExperimentalDesignUtils

public ExperimentalDesignUtils()

Method Detail

isComplete

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

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

Parameters:

samplesUsed - the samples used

factor - the factor

Returns:

false if there are any missing values.

getSampleToFactorValuesMap

public static Map<BioMaterial,Set<FactorValue>> getSampleToFactorValuesMap(ExperimentalFactor factor,
                                                                                 Collection<BioMaterial> samplesUsed)

Create a sample to factor value mapping.

Under normal circumstances, there should be only one factor value per sample.

buildDesignMatrix

public static ObjectMatrix<BioMaterial,ExperimentalFactor,Object> buildDesignMatrix(List<ExperimentalFactor> factors,
                                                                                                List<BioMaterial> samplesUsed,
                                                                                                boolean allowMissingValues)

Build a design matrix for the given factors and samples.

Parameters:

factors - factors

samplesUsed - the samples used

allowMissingValues - whether to allow missing values, if set to true, the returned matrix may contain nulls

Returns:

the experimental design matrix

Throws:

IllegalStateException - if missing values are found and allowMissingValues is false

buildRDesignMatrix

public static ObjectMatrix<String,String,Object> buildRDesignMatrix(List<ExperimentalFactor> factors,
                                                                                List<BioMaterial> samplesUsed,
                                                                                boolean allowMissingValues)

Build an R-friendly design matrix.

Rows and columns use names derived from nameForR(BioMaterial), nameForR(ExperimentalFactor) and nameForR(FactorValue, boolean) such that the resulting matrix can be passed to R for analysis. It is otherwise identical to buildDesignMatrix(List, List, boolean).

buildRDesignMatrix

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

A variant of buildRDesignMatrix(List, List, boolean) that allows for reusing baselines for repeated calls. This is used for subset analysis.

getBaselineConditions

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

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(Collection<ExperimentalFactor> factors,
                                                                          @Nullable
                                                                          List<BioMaterial> samplesUsed)

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:

factors - factors

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.

Returns:

map of factors to the baseline factorvalue for that factor.

measurement2double

public static double measurement2double(Measurement measurement)

Convert a measurement to a double. Missing values are treated as NaNs.

Throws:

UnsupportedOperationException - if the measurement representation is not supported

isBatchFactor

public static boolean isBatchFactor(ExperimentalFactor ef)

Check if a factor is a batch factor.

isBatchFactor

public static boolean isBatchFactor(ExperimentalFactorValueObject ef)

Check if a given factor VO is a batch factor.

nameForR

public static String nameForR(BioMaterial sample)

Create a name for a sample suitable for R.

nameForR

public static String nameForR(ExperimentalFactor experimentalFactor)

Create a name for the factor that is suitable for R.

nameForR

public static String nameForR(FactorValue fv,
                              boolean isBaseline)

Create a name for the factor value that is suitable for R.

getOrderedFactors

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

Sort factors in a consistent way.

For this to work, the factors must be persistent as the order will be based on the numerical ID.