Class OutlierDetectionServiceImpl
java.lang.Object
ubic.gemma.core.analysis.preprocess.OutlierDetectionServiceImpl
- All Implemented Interfaces:
OutlierDetectionService
Methods to (attempt to) detect outliers in data sets.
- Author:
- paul
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Constructor Summary
ConstructorsConstructorDescriptionOutlierDetectionServiceImpl(org.springframework.cache.CacheManager cacheManager) -
Method Summary
Modifier and TypeMethodDescriptionObtain existing outlier details from a previousOutlierDetectionService.identifyOutliersByMedianCorrelation(ExpressionExperiment)invocation.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.Identify outliers by median correlation for the given dataset.
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Constructor Details
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OutlierDetectionServiceImpl
@Autowired public OutlierDetectionServiceImpl(org.springframework.cache.CacheManager cacheManager)
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Method Details
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getOutlierDetails
Description copied from interface:OutlierDetectionServiceObtain existing outlier details from a previousOutlierDetectionService.identifyOutliersByMedianCorrelation(ExpressionExperiment)invocation.- Specified by:
getOutlierDetailsin interfaceOutlierDetectionService- Returns:
- outlier details or
Optional#empty()if no sample coexpression analysis exists
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identifyOutliersByMedianCorrelation
public Collection<OutlierDetails> identifyOutliersByMedianCorrelation(ExpressionExperiment ee) throws FilteringException Description copied from interface:OutlierDetectionServiceIdentify outliers by median correlation for the given dataset.- Specified by:
identifyOutliersByMedianCorrelationin interfaceOutlierDetectionService- Parameters:
ee- The experiment to identify sample outliers in.- Returns:
- the information about the identified outliers.
- Throws:
FilteringException- See Also:
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identifyOutliersByMedianCorrelation
public Collection<OutlierDetails> identifyOutliersByMedianCorrelation(DoubleMatrix<BioAssay, BioAssay> cormat) Description copied from interface:OutlierDetectionServiceIdentify 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:
identifyOutliersByMedianCorrelationin interfaceOutlierDetectionService- Parameters:
cormat- the correlation matrix to identify outliers in.- Returns:
- the information about the identified outliers.
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