Package fr.ens.biologie.genomique.eoulsan.modules.diffana

Class DESeq2Parameters

java.lang.Object
fr.ens.biologie.genomique.eoulsan.modules.diffana.DESeq2Parameters
public class DESeq2Parameters extends Object
This class contains DESeq2 module parameters.
Since:
2.7
Author:
Laurent Jourdren

  • Constructor Details

    • DESeq2Parameters

      public DESeq2Parameters()

  • Method Details

    • isNormFig

      public boolean isNormFig()
      Get the normFig parameter value.
      Returns:
      the normFig

    • isDiffanaFig

      public boolean isDiffanaFig()
      Get the diffanaFig parameter value.
      Returns:
      the diffanaFig

    • isNormDiffana

      public boolean isNormDiffana()
      Get the normDiffana parameter value.
      Returns:
      the normDiffana

    • isDiffana

      public boolean isDiffana()
      Get the diffana parameter value.
      Returns:
      the diffana

    • getSizeFactorsType

      public DESeq2Parameters.SizeFactorsType getSizeFactorsType()
      Get the sizeFactorsType parameter value.
      Returns:
      the sizeFactorsType

    • getFitType

      public DESeq2Parameters.FitType getFitType()
      Get the fitType parameter value.
      Returns:
      the fitType

    • getStatisticTest

      public DESeq2Parameters.StatisticTest getStatisticTest()
      Get the statisticTest parameter value.
      Returns:
      the statisticTest

    • isExpHeader

      public boolean isExpHeader()
      Get the expHeader parameter value.
      Returns:
      the expHeader

    • getEasyContrastsVersion

      public int getEasyContrastsVersion()
      Get the easy contrasts version to use.
      Returns:
      the easy contrasts version to use

    • isWeightContrast

      public boolean isWeightContrast()
      Get the weight contrast.
      Returns:
      the weightContrast

    • getLogoUrl

      public String getLogoUrl()
      Get the URL of the logo.
      Returns:
      the logoUrl

    • getAuthorName

      public String getAuthorName()
      Get the author Name.
      Returns:
      the author name

    • getAuthorEmail

      public String getAuthorEmail()
      Get the author email
      Returns:
      the author email

    • getAdjPValueThreshold

      public double getAdjPValueThreshold()
      Get the p-value adjusted threshold.
      Returns:
      the p-value adjusted threshold

    • getLog2FCThreshold

      public double getLog2FCThreshold()
      Get the log2 fold change threshold.
      Returns:
      the log2 fold change threshold

    • isSaveRDS

      public boolean isSaveRDS()
      Test if RDS file must be saved
      Returns:
      true if RDS file must be saved

    • isDisableNestedModels

      public boolean isDisableNestedModels()
      Test if RDS file must be saved
      Returns:
      true if RDS file must be saved

    • setNormFig

      public void setNormFig(boolean normFig)
      Set the normFig parameter value.
      Parameters:
      normFig - the normFig to set

    • setDiffanaFig

      public void setDiffanaFig(boolean diffanaFig)
      Set the diffanaFig parameter value.
      Parameters:
      diffanaFig - the diffanaFig to set

    • setNormDiffana

      public void setNormDiffana(boolean normDiffana)
      Set the normDiffana parameter value.
      Parameters:
      normDiffana - the normDiffana to set

    • setDiffana

      public void setDiffana(boolean diffana)
      Set the diffana parameter value.
      Parameters:
      diffana - the diffana to set

    • setSizeFactorsType

      public void setSizeFactorsType(String parameterName, String value) throws EoulsanException
      Set the size factors type parameter value.
      Parameters:
      parameterName - parameter name
      value - value to set
      Throws:
      EoulsanException - if the parameter value is not valid

    • setFitType

      public void setFitType(String parameterName, String value) throws EoulsanException
      Set the fit type parameter value.
      Parameters:
      parameterName - parameter name
      value - value to set
      Throws:
      EoulsanException - if the parameter value is not valid

    • setStatisticTest

      public void setStatisticTest(String parameterName, String value) throws EoulsanException
      Set the statistic test parameter value.
      Parameters:
      parameterName - parameter name
      value - value to set
      Throws:
      EoulsanException - if the parameter value is not valid

    • setExpHeader

      public void setExpHeader(boolean expHeader)
      Set the expHeader parameter value.
      Parameters:
      expHeader - the expHeader to set

    • setEasyContrastsVersion

      public void setEasyContrastsVersion(int version)
      Set the easy contrasts version to use.
      Parameters:
      version - the version

    • setWeightContrast

      public void setWeightContrast(boolean weightContrast)
      Set the weight contrast to use.
      Parameters:
      weightContrast - the weightContrast to set

    • setLogoUrl

      public void setLogoUrl(String logoUrl)
      Set the URL of the logo to use.
      Parameters:
      logoUrl - the logoUrl to set

    • setAuthorName

      public void setAuthorName(String authorName)
      Set the author name.
      Parameters:
      authorName - the authorName to set

    • setAuthorEmail

      public void setAuthorEmail(String authorEmail)
      Set the author email.
      Parameters:
      authorEmail - the authormail to set

    • setAdjPValueThreshold

      public void setAdjPValueThreshold(double padjLimit)
      Set the adjusted p-value threshold.
      Parameters:
      padjLimit - the adjusted p-value threshold to set

    • setLog2FCThreshold

      public void setLog2FCThreshold(double log2fcLimit)
      Set the log2 fold change threshold.
      Parameters:
      log2fcLimit - the log2 fold change threshold to set

    • setSaveRDS

      public void setSaveRDS(boolean saveRDS)
      Set save RDS.
      Parameters:
      saveRDS - the saveRDS to set

    • setDisableNestedModels

      public void setDisableNestedModels(boolean disabled)
      Disable nested models.
      Parameters:
      disabled - true to disable nested models

    • freeze

      public void freeze()
      Freeze the values in the object.

    • check

      public void check()
      Check DESeq2 parameters.