Uses of Interface
fr.ens.biologie.genomique.eoulsan.design.Experiment

Packages that use Experiment

Package	Description
fr.ens.biologie.genomique.eoulsan.checkers	This package contains and define checkers of DataFormat.
fr.ens.biologie.genomique.eoulsan.design	This package contains classes to handle experimental designs.
fr.ens.biologie.genomique.eoulsan.modules.diffana	This package contain all the classes related to the differential analysis step.

Uses of Experiment in fr.ens.biologie.genomique.eoulsan.checkers

Methods in fr.ens.biologie.genomique.eoulsan.checkers with parameters of type Experiment

Modifier and Type	Method	Description
static boolean	DESeq2DesignChecker.checkExperimentDesign(Experiment experiment)	Check experiment design.

Uses of Experiment in fr.ens.biologie.genomique.eoulsan.design

Classes in fr.ens.biologie.genomique.eoulsan.design that implement Experiment

Modifier and Type	Class	Description
class	ExperimentImpl	This class defines the default implementation of an experiment.
class	UnmodifiableExperiment

Methods in fr.ens.biologie.genomique.eoulsan.design that return Experiment

Modifier and Type	Method	Description
Experiment	Design.addExperiment(String experimentId)	Add an experiment.
Experiment	Design.getExperiment(String experimentId)	Get the name of an experiment.

Methods in fr.ens.biologie.genomique.eoulsan.design that return types with arguments of type Experiment

Modifier and Type	Method	Description
List<Experiment>	Design.getExperiments()	Get the list of the experiments.
List<Experiment>	Design.getExperimentsUsingASample(Sample sampleId)	Get all the experiments related to a sample.

Methods in fr.ens.biologie.genomique.eoulsan.design with parameters of type Experiment

Modifier and Type	Method	Description
static boolean	DesignUtils.containsReferenceField(Experiment experiment)	Test if an experiment contains reference fields
static String	DesignUtils.getCondition(Experiment experiment, Sample sample)	Get the Condition metadata value for an experimentSample.
static List<String>	DesignUtils.getExperimentSampleAllMetadataKeys(Experiment experiment)	Get all the experiment metadata keys of the samples of a design.
static String	DesignUtils.getMetadata(Experiment experiment, Sample sample, String key)	Get a metadata value for an experiment and a sample.
static Set<String>	DesignUtils.getModelColumns(Experiment experiment)	Get the column names used in DESeq2 model.
static String	DesignUtils.getReference(Experiment experiment, Sample sample)	Get the reference of a sample.
static String	DesignUtils.getRepTechGroup(Experiment experiment, Sample sample)	Get the RepTechGroup metadata value for an experimentSample.
static boolean	DesignUtils.isSkipped(Experiment experiment)	Test if an experiement is skipped.

Constructors in fr.ens.biologie.genomique.eoulsan.design with parameters of type Experiment

Constructor	Description
UnmodifiableExperiment(Experiment experiment)

Uses of Experiment in fr.ens.biologie.genomique.eoulsan.modules.diffana

Methods in fr.ens.biologie.genomique.eoulsan.modules.diffana with parameters of type Experiment

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

Constructors in fr.ens.biologie.genomique.eoulsan.modules.diffana with parameters of type Experiment

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.