Package ubic.gemma.model.analysis.expression.diff

Class GeneDifferentialExpressionMetaAnalysisResult

java.lang.Object

ubic.gemma.model.common.AbstractIdentifiable

ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisResult

All Implemented Interfaces:

Identifiable

public class GeneDifferentialExpressionMetaAnalysisResult
extends AbstractIdentifiable

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	GeneDifferentialExpressionMetaAnalysisResult.Factory

Constructor Summary

Constructors

Constructor	Description
GeneDifferentialExpressionMetaAnalysisResult()

Method Summary

Modifier and Type	Method	Description
boolean	equals(Object object)	Returns true if the argument is an GeneDifferentialExpressionMetaAnalysisResult instance and all identifiers for this entity equal the identifiers of the argument entity.
Gene	getGene()
Double	getMeanLogFoldChange()
Double	getMetaPvalue()
Double	getMetaPvalueRank()
Double	getMetaQvalue()
Set<DifferentialExpressionAnalysisResult>	getResultsUsed()
Boolean	getUpperTail()
int	hashCode()	Important note: Never use the ID in the hashCode() implementation since it can be assigned when the object is persisted.
void	setGene(Gene gene)
void	setMeanLogFoldChange(Double meanLogFoldChange)
void	setMetaPvalue(Double metaPvalue)
void	setMetaPvalueRank(Double metaPvalueRank)
void	setMetaQvalue(Double metaQvalue)
void	setResultsUsed(Set<DifferentialExpressionAnalysisResult> resultsUsed)
void	setUpperTail(Boolean upperTail)

Methods inherited from class ubic.gemma.model.common.AbstractIdentifiable

getId, setId, toString

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Constructor Detail

GeneDifferentialExpressionMetaAnalysisResult

public GeneDifferentialExpressionMetaAnalysisResult()

Method Detail

getGene

public Gene getGene()

setGene

public void setGene(Gene gene)

getMeanLogFoldChange

public Double getMeanLogFoldChange()

Returns:

Note that this value could be misleading; it is possible for the fold change to be positive but the meta-analysis is for down-regulation. Use 'upperTail' to see which direction was inspected.

setMeanLogFoldChange

public void setMeanLogFoldChange(Double meanLogFoldChange)

getMetaPvalue

public Double getMetaPvalue()

setMetaPvalue

public void setMetaPvalue(Double metaPvalue)

getMetaPvalueRank

public Double getMetaPvalueRank()

Returns:

The rank of the gene in the full set of results.

setMetaPvalueRank

public void setMetaPvalueRank(Double metaPvalueRank)

getMetaQvalue

public Double getMetaQvalue()

setMetaQvalue

public void setMetaQvalue(Double metaQvalue)

getResultsUsed

public Set<DifferentialExpressionAnalysisResult> getResultsUsed()

Returns:

The underlying differential expression results that contributed to the meta-analysis result.

setResultsUsed

public void setResultsUsed(Set<DifferentialExpressionAnalysisResult> resultsUsed)

getUpperTail

public Boolean getUpperTail()

Returns:

If true, indicates the fold change "looked for" was positive (i.e., pvalue measured using the upper tail of the t distribution; the alternative hypothesis is fold change > 0)

setUpperTail

public void setUpperTail(Boolean upperTail)

hashCode

public int hashCode()

Description copied from class: AbstractIdentifiable

Important note: Never use the ID in the hashCode() implementation since it can be assigned when the object is persisted.

Specified by:

hashCode in class AbstractIdentifiable

Returns:

a hash code based on this entity's identifiers.

equals

public boolean equals(Object object)

Returns true if the argument is an GeneDifferentialExpressionMetaAnalysisResult instance and all identifiers for this entity equal the identifiers of the argument entity. Returns false otherwise.

Specified by:

equals in class AbstractIdentifiable