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 enum	DiffAna.DispersionFitType	Dispersion estimation fitType enum for DESeq differential analysis
static enum	DiffAna.DispersionMethod	Dispersion estimation method enum for DESeq differential analysis
static enum	DiffAna.DispersionSharingMode	Dispersion estimation sharingMode enum for DESeq differential analysis

Constructor Summary

Constructors

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

Method Summary

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

run

Methods inherited from class java.lang.Object

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

Constructor Details

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