Class DESeq2
- java.lang.Object
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- fr.ens.biologie.genomique.eoulsan.modules.diffana.DESeq2
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public class DESeq2 extends Object
This class contains methods to run the differential analysis module DESeq2.- Since:
- 2.0
- Author:
- Xavier Bauquet
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Nested Class Summary
Nested Classes Modifier and Type Class Description static class
DESeq2.FitType
Enum for the fitType option in DESeq2 related to the dispersion estimation.static class
DESeq2.SizeFactorsType
Enum for the sizeFactorsType option in DESeq2 related to the estimation of the size factor.static class
DESeq2.StatisticTest
Enum for the statisticTest option in DESeq2 related to the statistic test to be used during the differential expression analysis
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Constructor Summary
Constructors Constructor Description 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.
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
runDEseq2(DataFile workflowOutputDir)
Method to run DESeq2.
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Constructor Detail
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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 iddesign
- the Eoulsan designexperiment
- the experimentsampleFiles
- the list of expression filesnormFig
- normFig DESeq2 optiondiffanaFig
- diffanaFig DESeq2 optionnormDiffana
- normDiffana DESeq2 optiondiffana
- diffana DESeq2 optionsizeFactorsType
- sizeFactorsType DESeq2 optionfitType
- fitType DESeq2 optionstatisticTest
- statisticTest DESeq2 option
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Method Detail
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runDEseq2
public void runDEseq2(DataFile workflowOutputDir) throws IOException, EoulsanException
Method to run DESeq2.- Parameters:
workflowOutputDir
- workflow output directory- Throws:
IOException
- if writeDeseq2Design failsEoulsanException
- if the comparisons value is not correct
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