Uses of Class
eu.isas.reporter.settings.RatioEstimationSettings

Packages that use RatioEstimationSettings
Package
Description
eu.isas.reporter
Main package.
eu.isas.reporter.calculation
Package containing classes used for the calculation.
eu.isas.reporter.calculation.normalization
Package containing classes used for the quantification.
eu.isas.reporter.gui.settings.quantification
Package containing GUI classes used for the edition of the quantification settings.
eu.isas.reporter.settings
Package containing the different settings.

  • Uses of RatioEstimationSettings in eu.isas.reporter

    Methods in eu.isas.reporter with parameters of type RatioEstimationSettings
    Modifier and Type
    Method
    Description
    static PeptideQuantificationDetails
    Reporter.estimatePeptideMatchQuantificationDetails(com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, QuantificationFeaturesGenerator quantificationFeaturesGenerator, RatioEstimationSettings ratioEstimationSettings, com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification reporterIonQuantification, com.compomics.util.experiment.identification.matches.PeptideMatch peptideMatch, com.compomics.util.waiting.WaitingHandler waitingHandler)
    Returns the quantification details of a peptide match.
    static ProteinQuantificationDetails
    Reporter.estimateProteinMatchQuantificationDetails(com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator identificationFeaturesGenerator, QuantificationFeaturesGenerator quantificationFeaturesGenerator, RatioEstimationSettings ratioEstimationSettings, com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification reporterIonQuantification, com.compomics.util.parameters.identification.search.SearchParameters searchParameters, com.compomics.util.experiment.identification.matches.ProteinMatch proteinMatch, com.compomics.util.waiting.WaitingHandler waitingHandler)
    Returns the quantification details of a protein match.
    static PsmQuantificationDetails
    Reporter.estimatePSMQuantificationDetails(com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, QuantificationFeaturesGenerator quantificationFeaturesGenerator, ReporterIonSelectionSettings reporterIonSelectionSettings, RatioEstimationSettings ratioEstimationSettings, com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification reporterIonQuantification, Long matchKey)
    Returns the quantification details of a PSM.
    static ProteinPtmQuantificationDetails
    Reporter.estimatePTMQuantificationDetails(com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, QuantificationFeaturesGenerator quantificationFeaturesGenerator, RatioEstimationSettings ratioEstimationSettings, com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification reporterIonQuantification, com.compomics.util.parameters.identification.search.SearchParameters searchParameters, com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters sequenceMatchingParameters, String ptmName, long matchKey, int site, com.compomics.util.waiting.WaitingHandler waitingHandler)
    Returns the quantification details of a PTM on a protein.//@TODO: discriminate peptides according to the neighboring sites?

  • Uses of RatioEstimationSettings in eu.isas.reporter.calculation

    Methods in eu.isas.reporter.calculation with parameters of type RatioEstimationSettings
    Modifier and Type
    Method
    Description
    static Double
    RatioEstimator.estimateRatios(RatioEstimationSettings ratioEstimationSettings, ArrayList<Double> ratios)
    Estimate the ratio resulting from the compilation of several ratios.
    static boolean
    QuantificationFilter.isPeptideValid(RatioEstimationSettings ratioEstimationSettings, com.compomics.util.experiment.identification.Identification identification, com.compomics.util.parameters.identification.search.SearchParameters searchParameters, com.compomics.util.experiment.identification.matches.PeptideMatch peptideMatch)
    Filters the peptide to be used for quantification according to the user quantification preferences.
    static boolean
    QuantificationFilter.isProteinValid(RatioEstimationSettings ratioEstimationSettings, com.compomics.util.experiment.identification.Identification identification, long matchKey)
    Filters the protein to be used for quantification according to the user quantification preferences.
    static boolean
    QuantificationFilter.isPsmValid(RatioEstimationSettings ratioEstimationSettings, com.compomics.util.experiment.identification.Identification identification, long matchKey)
    Filters the PSMs to be used for quantification according to the user quantification preferences.
    static boolean
    QuantificationFilter.isRatioValid(RatioEstimationSettings ratioEstimationSettings, Double ratio)
    Filters out NaN and 0 ratios.
    static Double
    RatioEstimator.mEstimate(RatioEstimationSettings ratioEstimationSettings, double[] ratios)
    Returns the compilation of various ratios using a redescending M-estimator.

  • Uses of RatioEstimationSettings in eu.isas.reporter.calculation.normalization

    Methods in eu.isas.reporter.calculation.normalization with parameters of type RatioEstimationSettings
    Modifier and Type
    Method
    Description
    void
    Normalizer.setPeptideNormalizationFactors(com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification reporterIonQuantification, RatioEstimationSettings ratioEstimationSettings, NormalizationSettings normalizationSettings, com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters sequenceMatchingParameters, com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, QuantificationFeaturesGenerator quantificationFeaturesGenerator, com.compomics.util.parameters.tools.ProcessingParameters processingParameters, com.compomics.util.parameters.identification.search.SearchParameters searchParameters, com.compomics.util.experiment.io.biology.protein.FastaParameters fastaParameters, com.compomics.util.parameters.identification.advanced.PeptideVariantsParameters peptideVariantsPreferences, com.compomics.util.exceptions.ExceptionHandler exceptionHandler, com.compomics.util.waiting.WaitingHandler waitingHandler)
    Sets the peptide normalization factors in the ReporterIonQuantification object.
    void
    Normalizer.setProteinNormalizationFactors(com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification reporterIonQuantification, RatioEstimationSettings ratioEstimationSettings, NormalizationSettings normalizationSettings, com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.experiment.identification.peptide_shaker.Metrics metrics, QuantificationFeaturesGenerator quantificationFeaturesGenerator, com.compomics.util.parameters.tools.ProcessingParameters processingParameters, com.compomics.util.parameters.identification.search.SearchParameters searchParameters, com.compomics.util.experiment.io.biology.protein.FastaParameters fastaParameters, com.compomics.util.parameters.identification.advanced.PeptideVariantsParameters peptideVariantsPreferences, com.compomics.util.exceptions.ExceptionHandler exceptionHandler, com.compomics.util.waiting.WaitingHandler waitingHandler)
    Sets the protein normalization factors in the ReporterIonQuantification object.
    void
    Normalizer.setPsmNormalizationFactors(com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification reporterIonQuantification, RatioEstimationSettings ratioEstimationSettings, NormalizationSettings normalizationSettings, com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters sequenceMatchingParameters, com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, QuantificationFeaturesGenerator quantificationFeaturesGenerator, com.compomics.util.parameters.tools.ProcessingParameters processingParameters, com.compomics.util.parameters.identification.search.SearchParameters searchParameters, com.compomics.util.experiment.io.biology.protein.FastaParameters fastaParameters, com.compomics.util.parameters.identification.advanced.PeptideVariantsParameters peptideVariantsPreferences, com.compomics.util.exceptions.ExceptionHandler exceptionHandler, com.compomics.util.waiting.WaitingHandler waitingHandler)
    Sets the PSM normalization factors in the ReporterIonQuantification object.

  • Uses of RatioEstimationSettings in eu.isas.reporter.gui.settings.quantification

    Methods in eu.isas.reporter.gui.settings.quantification that return RatioEstimationSettings
    Modifier and Type
    Method
    Description
    RatioEstimationSettings
    RatioEstimationSettingsDialog.getRatioEstimationSettings()
    Returns the settings as set by the user.
    Constructors in eu.isas.reporter.gui.settings.quantification with parameters of type RatioEstimationSettings
    Modifier
    Constructor
    Description
     
    RatioEstimationSettingsDialog(JDialog parentDialog, RatioEstimationSettings ratioEstimationSettings, com.compomics.util.parameters.identification.search.ModificationParameters modificationParameters, boolean editable)
    Creates a new RatioEstimationSettingsDialog.

  • Uses of RatioEstimationSettings in eu.isas.reporter.settings

    Methods in eu.isas.reporter.settings that return RatioEstimationSettings
    Modifier and Type
    Method
    Description
    RatioEstimationSettings
    RatioEstimationSettings.clone()
     
    RatioEstimationSettings
    ReporterSettings.getRatioEstimationSettings()
    Returns the ratio estimation settings.
    Methods in eu.isas.reporter.settings with parameters of type RatioEstimationSettings
    Modifier and Type
    Method
    Description
    boolean
    RatioEstimationSettings.isSameAs(RatioEstimationSettings anotherSetting)
    Indicates whether another setting is the same as this one.
    void
    ReporterSettings.setRatioEstimationSettings(RatioEstimationSettings ratioEstimationSettings)
    Sets the ratio estimation settings.