Class DESeq2


  • public class DESeq2
    extends Object
    This class contains methods to run the differential analysis module DESeq2.
    Since:
    2.0
    Author:
    Xavier Bauquet
    • Constructor Detail

      • DESeq2

        public DESeq2​(RExecutor executor,
                      String stepId,
                      Design design,
                      Experiment experiment,
                      Map<String,​File> sampleFiles,
                      boolean normFig,
                      boolean diffanaFig,
                      boolean normDiffana,
                      boolean diffana,
                      DESeq2.SizeFactorsType sizeFactorsType,
                      DESeq2.FitType fitType,
                      DESeq2.StatisticTest statisticTest,
                      boolean saveRScripts)
        Public constructor.
        Parameters:
        stepId - the step id
        design - the Eoulsan design
        experiment - the experiment
        sampleFiles - the list of expression files
        normFig - normFig DESeq2 option
        diffanaFig - diffanaFig DESeq2 option
        normDiffana - normDiffana DESeq2 option
        diffana - diffana DESeq2 option
        sizeFactorsType - sizeFactorsType DESeq2 option
        fitType - fitType DESeq2 option
        statisticTest - statisticTest DESeq2 option