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

Class DESeq2

java.lang.Object

fr.ens.biologie.genomique.eoulsan.modules.diffana.DESeq2

public class DESeq2
extends Object

This class contains methods to run the differential analysis module DESeq2.

Since:

2.0

Author:

Xavier Bauquet

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

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.

Method Summary

Modifier and Type	Method	Description
void	runDEseq2(DataFile workflowOutputDir)	Method to run DESeq2.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

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

Method Detail

runDEseq2

public void runDEseq2(DataFile workflowOutputDir)
               throws IOException,
                      EoulsanException

Method to run DESeq2.

Parameters:

workflowOutputDir - workflow output directory

Throws:

IOException - if writeDeseq2Design fails

EoulsanException - if the comparisons value is not correct