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

Class ExpressionExperimentBatchInformationServiceImpl

java.lang.Object

ubic.gemma.core.analysis.preprocess.batcheffects.ExpressionExperimentBatchInformationServiceImpl

All Implemented Interfaces:

ExpressionExperimentBatchInformationService

@Service
public class ExpressionExperimentBatchInformationServiceImpl
extends Object
implements ExpressionExperimentBatchInformationService

Constructor Summary

Constructors

Constructor	Description
ExpressionExperimentBatchInformationServiceImpl()

Method Summary

Modifier and Type	Method	Description
boolean	checkHasBatchInfo(ExpressionExperiment ee)	Check if the given experiment has batch information.
boolean	checkHasUsableBatchInfo(ExpressionExperiment ee)	Check if the given experiment has usable batch information.
String	getBatchConfoundAsHtmlString(ExpressionExperiment ee)	Summarize the batch confounds for a given dataset or its subsets in an HTML string.
BatchEffectType	getBatchEffect(ExpressionExperiment ee)	Obtain a BatchEffectType describing the batch effect state of the given experiment.
BatchEffectDetails	getBatchEffectDetails(ExpressionExperiment ee)	Obtain the full batch effect details of a given experiment.
String	getBatchEffectStatistics(ExpressionExperiment ee)	Obtain a string describing the summary statistics of a batch effect is present in the given experiment.
List<BatchConfound>	getSignificantBatchConfounds(ExpressionExperiment ee)	Obtain the significant batch confounds for a dataset.
Map<ExpressionExperimentSubSet,List<BatchConfound>>	getSignificantBatchConfoundsForSubsets(ExpressionExperiment ee)	Obtain the significant batch confounds for a dataset subsets.
boolean	hasSignificantBatchConfound(ExpressionExperiment ee)	Check if a given experiment has a significant batch confound.

Methods inherited from class java.lang.Object

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

Constructor Detail

ExpressionExperimentBatchInformationServiceImpl

public ExpressionExperimentBatchInformationServiceImpl()

Method Detail

checkHasBatchInfo

@Transactional(readOnly=true)
public boolean checkHasBatchInfo(ExpressionExperiment ee)

Description copied from interface: ExpressionExperimentBatchInformationService

Check if the given experiment has batch information.

This does not imply that the batch information is usable or valid. Use ExpressionExperimentBatchInformationService.checkHasUsableBatchInfo(ExpressionExperiment) for that purpose.

Specified by:

checkHasBatchInfo in interface ExpressionExperimentBatchInformationService

checkHasUsableBatchInfo

@Transactional(readOnly=true)
public boolean checkHasUsableBatchInfo(ExpressionExperiment ee)

Description copied from interface: ExpressionExperimentBatchInformationService

Check if the given experiment has usable batch information.

Specified by:

checkHasUsableBatchInfo in interface ExpressionExperimentBatchInformationService

hasSignificantBatchConfound

@Transactional(readOnly=true)
public boolean hasSignificantBatchConfound(ExpressionExperiment ee)

Description copied from interface: ExpressionExperimentBatchInformationService

Check if a given experiment has a significant batch confound.

Specified by:

hasSignificantBatchConfound in interface ExpressionExperimentBatchInformationService

getSignificantBatchConfounds

@Transactional(readOnly=true)
public List<BatchConfound> getSignificantBatchConfounds(ExpressionExperiment ee)

Description copied from interface: ExpressionExperimentBatchInformationService

Obtain the significant batch confounds for a dataset.

Specified by:

getSignificantBatchConfounds in interface ExpressionExperimentBatchInformationService

getSignificantBatchConfoundsForSubsets

@Transactional(readOnly=true)
public Map<ExpressionExperimentSubSet,List<BatchConfound>> getSignificantBatchConfoundsForSubsets(ExpressionExperiment ee)

Description copied from interface: ExpressionExperimentBatchInformationService

Obtain the significant batch confounds for a dataset subsets.

Specified by:

getSignificantBatchConfoundsForSubsets in interface ExpressionExperimentBatchInformationService

getBatchConfoundAsHtmlString

@Transactional(readOnly=true)
public String getBatchConfoundAsHtmlString(ExpressionExperiment ee)

Description copied from interface: ExpressionExperimentBatchInformationService

Summarize the batch confounds for a given dataset or its subsets in an HTML string.

Specified by:

getBatchConfoundAsHtmlString in interface ExpressionExperimentBatchInformationService

Returns:

a summary or null if there is no batch confound

getBatchEffectDetails

@Transactional(readOnly=true)
public BatchEffectDetails getBatchEffectDetails(ExpressionExperiment ee)

Description copied from interface: ExpressionExperimentBatchInformationService

Obtain the full batch effect details of a given experiment.

Specified by:

getBatchEffectDetails in interface ExpressionExperimentBatchInformationService

Parameters:

ee - experiment

Returns:

details for the principal component most associated with batches (even if it isn't "significant"). Note that we don't look at every component, just the first few.

getBatchEffect

@Transactional(readOnly=true)
public BatchEffectType getBatchEffect(ExpressionExperiment ee)

Description copied from interface: ExpressionExperimentBatchInformationService

Obtain a BatchEffectType describing the batch effect state of the given experiment.

Specified by:

getBatchEffect in interface ExpressionExperimentBatchInformationService

Parameters:

ee - the experiment to get the batch effect for.

getBatchEffectStatistics

@Transactional(readOnly=true)
public String getBatchEffectStatistics(ExpressionExperiment ee)

Description copied from interface: ExpressionExperimentBatchInformationService

Obtain a string describing the summary statistics of a batch effect is present in the given experiment.

Specified by:

getBatchEffectStatistics in interface ExpressionExperimentBatchInformationService

Returns:

summary statistics or null if there is no batch effect