Interface GeneDifferentialExpressionService
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- All Known Implementing Classes:
GeneDifferentialExpressionServiceImpl
public interface GeneDifferentialExpressionService
- Author:
- paul
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Field Summary
Fields Modifier and Type Field Description static double
PVALUE_CLIP_THRESHOLD
p values smaller than this will be treated as this value in a meta-analysis.
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Method Summary
All Methods Instance Methods Abstract Methods Modifier and Type Method Description ExperimentalFactorValueObject
configExperimentalFactorValueObject(ExperimentalFactor ef)
ExpressionExperimentValueObject
configExpressionExperimentValueObject(ExpressionExperimentValueObject ee)
Collection<DifferentialExpressionValueObject>
getDifferentialExpression(Gene gene, double threshold, int limit)
Get the differential expression results for the given gene across all datasets.Collection<DifferentialExpressionValueObject>
getDifferentialExpression(Gene gene, double threshold, Collection<DiffExpressionSelectedFactorCommand> factorMap)
Get differential expression for a gene, constrained to a specific set of factors.Collection<DifferentialExpressionValueObject>
getDifferentialExpression(Gene gene, Collection<BioAssaySet> ees)
Get the differential expression results for the given gene that is in a specified set of experiments.Collection<DifferentialExpressionValueObject>
getDifferentialExpression(Gene gene, BioAssaySet ees, double threshold, int limit)
Get the differential expression results for the given gene that is in a specified set of experiments.DifferentialExpressionMetaAnalysisValueObject
getDifferentialExpressionMetaAnalysis(double threshold, Gene g, Map<Long,Long> eeFactorsMap, Collection<BioAssaySet> activeExperiments)
Get the differential expression analysis results for the gene in the activeExperiments.
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Field Detail
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PVALUE_CLIP_THRESHOLD
static final double PVALUE_CLIP_THRESHOLD
p values smaller than this will be treated as this value in a meta-analysis. The reason is to avoid extremely low pvalues from driving meta-pvalues down too fast. This is suggested by the fact that very small pvalues presume an extremely high precision in agreement between the tails of the true null distribution and the analytic distribution used to compute the pvalues (e.g., F or t).- See Also:
- Constant Field Values
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Method Detail
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configExperimentalFactorValueObject
ExperimentalFactorValueObject configExperimentalFactorValueObject(ExperimentalFactor ef)
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configExpressionExperimentValueObject
ExpressionExperimentValueObject configExpressionExperimentValueObject(ExpressionExperimentValueObject ee)
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getDifferentialExpression
Collection<DifferentialExpressionValueObject> getDifferentialExpression(Gene gene, Collection<BioAssaySet> ees)
Get the differential expression results for the given gene that is in a specified set of experiments.- Parameters:
gene
- : gene of interestees
- : set of experiments to search- Returns:
- DEA VOs
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getDifferentialExpression
Collection<DifferentialExpressionValueObject> getDifferentialExpression(Gene gene, BioAssaySet ees, double threshold, int limit)
Get the differential expression results for the given gene that is in a specified set of experiments.- Parameters:
gene
- : gene of interestees
- : set of experiments to searchthreshold
- : the cutoff to determine if diff expressedlimit
- : the maximum number of results to return (null for all)- Returns:
- DEA VOs
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getDifferentialExpression
Collection<DifferentialExpressionValueObject> getDifferentialExpression(Gene gene, double threshold, Collection<DiffExpressionSelectedFactorCommand> factorMap)
Get differential expression for a gene, constrained to a specific set of factors. Note that interactions are ignored, only main effects (the factorMap can only have one factor per experiment)- Parameters:
gene
- genethreshold
- thresholdfactorMap
- factor map- Returns:
- DEA VOs
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getDifferentialExpression
Collection<DifferentialExpressionValueObject> getDifferentialExpression(Gene gene, double threshold, int limit)
Get the differential expression results for the given gene across all datasets.- Parameters:
threshold
- thresholdgene
- genelimit
- limit- Returns:
- DEA VOs
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getDifferentialExpressionMetaAnalysis
DifferentialExpressionMetaAnalysisValueObject getDifferentialExpressionMetaAnalysis(double threshold, Gene g, Map<Long,Long> eeFactorsMap, Collection<BioAssaySet> activeExperiments)
Get the differential expression analysis results for the gene in the activeExperiments.- Parameters:
activeExperiments
- active eeseeFactorsMap
- factor mapg
- genethreshold
- threshold- Returns:
- diff exp. analysis meta VO
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