Package ubic.gemma.core.analysis.expression.coexpression.links

Class LinkAnalysisConfig

java.lang.Object
ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysisConfig
All Implemented Interfaces:
Serializable
public class LinkAnalysisConfig extends Object implements Serializable
Holds parameters needed for LinkAnalysis. Note that many of these settings are not typically changed from the defaults; they are there for experimentation.
Author:
Paul
See Also:

  • Field Details

    • DEFAULT_PROBE_DEGREE_THRESHOLD

      public static final Integer DEFAULT_PROBE_DEGREE_THRESHOLD
      probes with more links than this are ignored. Zero means this doesn't do anything.

  • Constructor Details

    • LinkAnalysisConfig

      public LinkAnalysisConfig()

  • Method Details

    • isCheckForBatchEffect

      public boolean isCheckForBatchEffect()

    • setCheckForBatchEffect

      public void setCheckForBatchEffect(boolean rejectForBatchEffect)

    • isCheckForOutliers

      public boolean isCheckForOutliers()

    • setCheckForOutliers

      public void setCheckForOutliers(boolean rejectForOutliers)

    • getArrayName

      public String getArrayName()

    • setArrayName

      public void setArrayName(String arrayName)

    • getCdfCut

      public double getCdfCut()

    • setCdfCut

      public void setCdfCut(double cdfCut)

    • getCorrelationCacheThreshold

      public double getCorrelationCacheThreshold()

    • setCorrelationCacheThreshold

      public void setCorrelationCacheThreshold(double correlationCacheThreshold)

    • getFwe

      public double getFwe()

    • setFwe

      public void setFwe(double fwe)

    • getLowerTailCut

      public double getLowerTailCut()

    • setLowerTailCut

      public void setLowerTailCut(double lowerTailCut)

    • getMetric

      public String getMetric()

    • setMetric

      public void setMetric(String metric)

    • getMinNumPresent

      public int getMinNumPresent()

    • setMinNumPresent

      public void setMinNumPresent(int minNumPresent)

    • getNormalizationMethod

      public LinkAnalysisConfig.NormalizationMethod getNormalizationMethod()
      Returns:
      the normalizationMethod

    • setNormalizationMethod

      public void setNormalizationMethod(LinkAnalysisConfig.NormalizationMethod normalizationMethod)
      Parameters:
      normalizationMethod - the normalizationMethod to set

    • getOutputFile

      public File getOutputFile()

    • setOutputFile

      public void setOutputFile(File outputFile)

    • getProbeDegreeThreshold

      public Integer getProbeDegreeThreshold()

    • setProbeDegreeThreshold

      public void setProbeDegreeThreshold(int probeDegreeThreshold)
      Probe degree threshold: Probes with more than this number of links are ignored. If set to <= 0, this setting is ignored.
      Parameters:
      probeDegreeThreshold - the probeDegreeThreshold to set

    • getSingularThreshold

      public LinkAnalysisConfig.SingularThreshold getSingularThreshold()
      Returns:
      the singularThreshold

    • setSingularThreshold

      public void setSingularThreshold(LinkAnalysisConfig.SingularThreshold singularThreshold)
      Set to modify threshold behaviour: enforce the choice of only one of the two standard thresholds.
      Parameters:
      singularThreshold - the singularThreshold to set. Default is 'none'.

    • getSubsetSize

      public double getSubsetSize()

    • setSubsetSize

      public void setSubsetSize(double subsetSize)

    • getUpperTailCut

      public double getUpperTailCut()

    • setUpperTailCut

      public void setUpperTailCut(double upperTailCut)

    • isAbsoluteValue

      public boolean isAbsoluteValue()

    • setAbsoluteValue

      public void setAbsoluteValue(boolean absoluteValue)

    • isCheckCorrelationDistribution

      public boolean isCheckCorrelationDistribution()

    • setCheckCorrelationDistribution

      public void setCheckCorrelationDistribution(boolean checkCorrelationDistribution)

    • isLowerCdfCutUsed

      public boolean isLowerCdfCutUsed()
      Returns:
      the lowerCdfCutUsed

    • setLowerCdfCutUsed

      public void setLowerCdfCutUsed(boolean lowerCdfCutUsed)
      Parameters:
      lowerCdfCutUsed - the lowerCdfCutUsed to set

    • isMakeSampleCorrMatImages

      public boolean isMakeSampleCorrMatImages()

    • setMakeSampleCorrMatImages

      public void setMakeSampleCorrMatImages(boolean makeSampleCorrMatImages)

    • isOmitNegLinks

      public boolean isOmitNegLinks()
      Returns:
      the omitNegLinks

    • setOmitNegLinks

      public void setOmitNegLinks(boolean omitNegLinks)
      Parameters:
      omitNegLinks - the omitNegLinks to set

    • isSubset

      public boolean isSubset()

    • setSubset

      public void setSubset(boolean subset)

    • isSubsetUsed

      public boolean isSubsetUsed()

    • setSubsetUsed

      public void setSubsetUsed(boolean subsetUsed)

    • isTextOut

      public boolean isTextOut()

    • setTextOut

      public void setTextOut(boolean b)

    • isUpperCdfCutUsed

      public boolean isUpperCdfCutUsed()
      Returns:
      the upperCdfCutUsed

    • setUpperCdfCutUsed

      public void setUpperCdfCutUsed(boolean upperCdfCutUsed)
      Parameters:
      upperCdfCutUsed - the upperCdfCutUsed to set

    • isUseDb

      public boolean isUseDb()

    • setUseDb

      public void setUseDb(boolean useDb)

    • isLogTransform

      public boolean isLogTransform()

    • setLogTransform

      public void setLogTransform(boolean logTransform)

    • toAnalysis

      public CoexpressionAnalysis toAnalysis()
      Returns:
      representation of this analysis (not completely filled in - only the basic parameters)

    • toString

      public String toString()
      Overrides:
      toString in class Object