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

Class DiffAna

java.lang.Object

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

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

public class DiffAna
extends Normalization

This class create and launch a R script to compute differential analysis.

Since:

1.0

Author:

Laurent Jourdren, Vivien Deshaies

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	DiffAna.DispersionFitType	Dispersion estimation fitType enum for DESeq differential analysis
static class	DiffAna.DispersionMethod	Dispersion estimation method enum for DESeq differential analysis
static class	DiffAna.DispersionSharingMode	Dispersion estimation sharingMode enum for DESeq differential analysis

Field Summary

Fields inherited from class fr.ens.biologie.genomique.eoulsan.modules.diffana.Normalization

design, executor, expressionFilesPrefix, expressionFilesSuffix, NORMALIZATION_FUNCTIONS, rConnection, TARGET_CREATION

Constructor Summary

Constructors

Constructor	Description
DiffAna(RExecutor executor, Design design, DiffAna.DispersionMethod dispEstMethod, DiffAna.DispersionSharingMode dispEstSharingMode, DiffAna.DispersionFitType dispEstFitType)	Public constructor.

Method Summary

Modifier and Type	Method	Description
protected String	generateScript(Experiment experiment, TaskContext context)	Generate the R script.

Methods inherited from class fr.ens.biologie.genomique.eoulsan.modules.diffana.Normalization

checkRepTechGroupCoherence, escapeUnderScore, generateConditionPart, generateExpressionFileNamesPart, generateRepTechGroupPart, generateRnwpreamble, generateSampleIdsPart, generateSampleNamePart, isTechnicalReplicates, readStaticScript, replaceRtgNA, run, runRExecutor

Methods inherited from class java.lang.Object

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

Constructor Detail

DiffAna

public DiffAna(RExecutor executor,
               Design design,
               DiffAna.DispersionMethod dispEstMethod,
               DiffAna.DispersionSharingMode dispEstSharingMode,
               DiffAna.DispersionFitType dispEstFitType)
        throws EoulsanException

Public constructor.

Parameters:

executor - executor to use to execute the differential analysis

design - The design object

dispEstMethod - dispersion estimation method

dispEstSharingMode - dispersion estimation sharing mode

dispEstFitType - dispersion estimation fit type

Throws:

EoulsanException - if an error occurs if connection to RServe server cannot be established

Method Detail

generateScript

protected String generateScript(Experiment experiment,
                                TaskContext context)
                         throws EoulsanException

Description copied from class: Normalization

Generate the R script.

Overrides:

generateScript in class Normalization

Parameters:

experiment - the experiment

context - step context

Returns:

String rScript R script to execute

Throws:

EoulsanException - if an error occurs while generate the R script