Package ubic.gemma.core.analysis.preprocess

Class OutlierDetectionServiceImpl

java.lang.Object

ubic.gemma.core.analysis.preprocess.OutlierDetectionServiceImpl

All Implemented Interfaces:

OutlierDetectionService

@Service
public class OutlierDetectionServiceImpl
extends Object
implements OutlierDetectionService

Methods to (attempt to) detect outliers in data sets.

Author:

paul

Constructor Summary

Constructors

Constructor	Description
OutlierDetectionServiceImpl(org.springframework.cache.CacheManager cacheManager)

Method Summary

Modifier and Type	Method	Description
Optional<Collection<OutlierDetails>>	getOutlierDetails(ExpressionExperiment ee)	Obtain existing outlier details from a previous OutlierDetectionService.identifyOutliersByMedianCorrelation(ExpressionExperiment) invocation.
Collection<OutlierDetails>	identifyOutliersByMedianCorrelation(DoubleMatrix<BioAssay,BioAssay> cormat)	Identify outliers by sorting by median, then looking for non-overlap of first quartile-second quartile range This is exposed for efficiency in geeq score calculation, use this#identifyOutliers(ExpressionExperiment, boolean, boolean) to have the correlation matrix computed correctly for you.
Collection<OutlierDetails>	identifyOutliersByMedianCorrelation(ExpressionExperiment ee)	Identify outliers by median correlation for the given dataset.

Methods inherited from class java.lang.Object

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

Constructor Details

OutlierDetectionServiceImpl

@Autowired
public OutlierDetectionServiceImpl(org.springframework.cache.CacheManager cacheManager)

Method Details

getOutlierDetails

public Optional<Collection<OutlierDetails>> getOutlierDetails(ExpressionExperiment ee)

Description copied from interface: OutlierDetectionService

Obtain existing outlier details from a previous OutlierDetectionService.identifyOutliersByMedianCorrelation(ExpressionExperiment) invocation.

Specified by:

getOutlierDetails in interface OutlierDetectionService

Returns:

outlier details or Optional#empty() if no sample coexpression analysis exists

identifyOutliersByMedianCorrelation

public Collection<OutlierDetails> identifyOutliersByMedianCorrelation(ExpressionExperiment ee)
                                                               throws FilteringException

Description copied from interface: OutlierDetectionService

Identify outliers by median correlation for the given dataset.

Specified by:

identifyOutliersByMedianCorrelation in interface OutlierDetectionService

Parameters:

ee - The experiment to identify sample outliers in.

Returns:

the information about the identified outliers.

Throws:

FilteringException

See Also:

• OutlierDetectionService.identifyOutliersByMedianCorrelation(DoubleMatrix)

identifyOutliersByMedianCorrelation

public Collection<OutlierDetails> identifyOutliersByMedianCorrelation(DoubleMatrix<BioAssay,BioAssay> cormat)

Description copied from interface: OutlierDetectionService

Identify outliers by sorting by median, then looking for non-overlap of first quartile-second quartile range This is exposed for efficiency in geeq score calculation, use this#identifyOutliers(ExpressionExperiment, boolean, boolean) to have the correlation matrix computed correctly for you.

Specified by:

identifyOutliersByMedianCorrelation in interface OutlierDetectionService

Parameters:

cormat - the correlation matrix to identify outliers in.

Returns:

the information about the identified outliers.