Class NormalizationFactors

java.lang.Object
com.compomics.util.experiment.normalization.NormalizationFactors

public class NormalizationFactors
extends Object
Class grouping the normalization factors used to normalize quantification results.
Author:
Marc Vaudel
  • Constructor Details

  • Method Details

    • hasNormalizationFactors

      public boolean hasNormalizationFactors()
      Indicates whether normalization factors are set.
      Returns:
      a boolean indicating whether the protein normalization factors are set
    • hasProteinNormalisationFactors

      public boolean hasProteinNormalisationFactors()
      Indicates whether the protein normalization factors are set.
      Returns:
      a boolean indicating whether the protein normalization factors are set
    • hasPeptideNormalisationFactors

      public boolean hasPeptideNormalisationFactors()
      Indicates whether the peptide normalization factors are set.
      Returns:
      a boolean indicating whether the peptide normalization factors are set
    • hasPsmNormalisationFactors

      public boolean hasPsmNormalisationFactors()
      Indicates whether the PSM normalization factors are set.
      Returns:
      a boolean indicating whether the PSM normalization factors are set
    • resetProteinNormalisationFactors

      public void resetProteinNormalisationFactors()
      Resets the protein normalization factors.
    • resetPeptideNormalisationFactors

      public void resetPeptideNormalisationFactors()
      Resets the peptide normalization factors.
    • resetPsmNormalisationFactors

      public void resetPsmNormalisationFactors()
      Resets the PSM normalization factors.
    • addProteinNormalisationFactor

      public void addProteinNormalisationFactor​(String sampleName, double normalisationFactor)
      Adds a protein normalization factor.
      Parameters:
      sampleName - the index of the sample
      normalisationFactor - the normalization factor
    • addPeptideNormalisationFactor

      public void addPeptideNormalisationFactor​(String sampleName, double normalisationFactor)
      Adds a peptide normalization factor.
      Parameters:
      sampleName - the index of the sample
      normalisationFactor - the normalization factor
    • addPsmNormalisationFactor

      public void addPsmNormalisationFactor​(String sampleName, double normalisationFactor)
      Adds a PSM normalization factor.
      Parameters:
      sampleName - the index of the sample
      normalisationFactor - the normalization factor
    • getProteinNormalisationFactor

      public double getProteinNormalisationFactor​(String sampleName)
      Returns the protein normalization factor for the given sample, 1.0 if not set.
      Parameters:
      sampleName - the index of the sample
      Returns:
      the normalization factor
    • getPeptideNormalisationFactor

      public double getPeptideNormalisationFactor​(String sampleName)
      Returns the peptide normalization factor for the given sample, 1.0 if not set.
      Parameters:
      sampleName - the index of the sample
      Returns:
      the normalization factor
    • getPsmNormalisationFactor

      public double getPsmNormalisationFactor​(String sampleName)
      Returns the PSM normalization factor for the given sample, 1.0 if not set.
      Parameters:
      sampleName - the index of the sample
      Returns:
      the normalization factor