Package ubic.gemma.core.analysis.preprocess.batcheffects

Class BatchEffectDetails

java.lang.Object

ubic.gemma.core.analysis.preprocess.batcheffects.BatchEffectDetails

public class BatchEffectDetails
extends Object

provide some basic information about the properties and strength of a batch effect, if any.

Author:

Paul

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
class	BatchEffectDetails.BatchEffectStatistics

Constructor Summary

Constructors

Constructor	Description
BatchEffectDetails(BatchInformationEvent infoEvent, boolean dataWasBatchCorrected, boolean singleBatch)

Method Summary

Modifier and Type	Method	Description
boolean	dataWasBatchCorrected()	Indicate if batch correction was performed on the expression data.
BatchEffectDetails.BatchEffectStatistics	getBatchEffectStatistics()	Obtain an object describing the batch effect if available.
boolean	hasBatchInformation()	Indicate if the batch information is present.
boolean	hasProblematicBatchInformation()	Indicate if the batch information is present, but problematic.
boolean	hasSingletonBatches()	Indicate if the dataset has one or more singleton batches (i.e.
boolean	hasUninformativeBatchInformation()	Indicate if the batch information is present, but uninformative.
boolean	isSingleBatch()	Indicate if the experiment was determined to have just one batch, or false for any other state (including we don't know).
void	setBatchEffectStatistics(double pVal, int i, double variance)	Set the batch effect statistics.
String	toString()

Methods inherited from class java.lang.Object

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

Constructor Detail

BatchEffectDetails

public BatchEffectDetails(@Nullable
                          BatchInformationEvent infoEvent,
                          boolean dataWasBatchCorrected,
                          boolean singleBatch)

Method Detail

hasBatchInformation

public boolean hasBatchInformation()

Indicate if the batch information is present.

hasProblematicBatchInformation

public boolean hasProblematicBatchInformation()

Indicate if the batch information is present, but problematic.

hasUninformativeBatchInformation

public boolean hasUninformativeBatchInformation()

Indicate if the batch information is present, but uninformative.

hasSingletonBatches

public boolean hasSingletonBatches()

Indicate if the dataset has one or more singleton batches (i.e. a batch with only one sample).

isSingleBatch

public boolean isSingleBatch()

Indicate if the experiment was determined to have just one batch, or false for any other state (including we don't know).

dataWasBatchCorrected

public boolean dataWasBatchCorrected()

Indicate if batch correction was performed on the expression data.

getBatchEffectStatistics

@Nullable
public BatchEffectDetails.BatchEffectStatistics getBatchEffectStatistics()

Obtain an object describing the batch effect if available.

setBatchEffectStatistics

public void setBatchEffectStatistics(double pVal,
                                     int i,
                                     double variance)

Set the batch effect statistics.

Parameters:

pVal - P-value

i - component connfounded by the bat

variance - variance explained by the component

toString

public String toString()

Overrides:

toString in class Object