Class LinkAnalysis
- java.lang.Object
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- ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysis
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public class LinkAnalysis extends Object
Handles the actual coexpression analysis, once handed data that has been prepared. Results are made available at the end. See LinkAnalysisCli for more instructions. This should be created for each analysis - it's not reusable.- Author:
- xiangwan, paul (refactoring)
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Field Summary
Fields Modifier and Type Field Description protected static org.apache.commons.logging.Log
log
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Constructor Summary
Constructors Constructor Description LinkAnalysis(LinkAnalysisConfig config)
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Method Summary
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Constructor Detail
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LinkAnalysis
public LinkAnalysis(LinkAnalysisConfig config)
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Method Detail
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analyze
public void analyze()
Main entry point.
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clear
public void clear()
Clear/null data so this object can be reused.
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getAnalysisObj
public CoexpressionAnalysis getAnalysisObj()
- Returns:
- object containing the parameters used.
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setAnalysisObj
public void setAnalysisObj(CoexpressionAnalysis analysis)
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getConfig
public LinkAnalysisConfig getConfig()
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getCorrelationDistribution
public CoexpCorrelationDistribution getCorrelationDistribution()
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getDataMatrix
public ExpressionDataDoubleMatrix getDataMatrix()
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setDataMatrix
public void setDataMatrix(ExpressionDataDoubleMatrix paraDataMatrix)
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getExpressionExperiment
public BioAssaySet getExpressionExperiment()
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setExpressionExperiment
public void setExpressionExperiment(BioAssaySet expressionExperiment)
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getGenesTested
public Set<Gene> getGenesTested()
Gene the genes that were tested, according to the rows that are currently in the dataMatrix (so call this after filtering!)- Returns:
- set
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getKeep
public ObjectArrayList getKeep()
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getMetric
public QuantitationType getMetric()
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getMetricMatrix
public MatrixRowPairAnalysis getMetricMatrix()
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getProbe
public CompositeSequence getProbe(int index)
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getProbeDegree
public Integer getProbeDegree(int index)
- Parameters:
index
- row number in the metrixMatirx- Returns:
- how many Links that probe appears in, or null if the probeDegree has not been populated for that index (that is, either to early to check, or it was zero).
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getProbeToGeneMap
public Map<CompositeSequence,Set<Gene>> getProbeToGeneMap()
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setProbeToGeneMap
public void setProbeToGeneMap(Map<CompositeSequence,Set<Gene>> probeToGeneMap)
Once set, is unmodifiable.- Parameters:
probeToGeneMap
- map
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getTaxon
public Taxon getTaxon()
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setTaxon
public void setTaxon(Taxon taxon)
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