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

Class 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:
    Serialized Form

    • Field Detail

      • 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 Detail

      • LinkAnalysisConfig

        public LinkAnalysisConfig()

    • Method Detail

      • 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)

      • 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

      • 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)

      • toAnalysis

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