Uses of Interface
fr.ens.biologie.genomique.eoulsan.util.r.RExecutor

Packages that use RExecutor

Package	Description
fr.ens.biologie.genomique.eoulsan.modules.diffana	This package contain all the classes related to the differential analysis step.
fr.ens.biologie.genomique.eoulsan.util.r	This package contain utility classes for R usage.

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

Fields in fr.ens.biologie.genomique.eoulsan.modules.diffana declared as RExecutor

Modifier and Type	Field	Description
protected RExecutor	Normalization.executor

Methods in fr.ens.biologie.genomique.eoulsan.modules.diffana that return RExecutor

Modifier and Type	Method	Description
static RExecutor	RModuleCommonConfiguration.parseRExecutorParameter(StepConfigurationContext context, Set<Parameter> stepParameters, Set<Requirement> requirements, String defaultDockerImage)	Parse the step parameter and create a configured RExecutor object.

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

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

Uses of RExecutor in fr.ens.biologie.genomique.eoulsan.util.r

Classes in fr.ens.biologie.genomique.eoulsan.util.r that implement RExecutor

Modifier and Type	Class	Description
class	AbstractRExecutor	This class define an abstract RExecutor.
class	DockerRExecutor	This class define a Docker RExecutor.
class	ProcessRExecutor	This class define a standard RExecutor using a system process.
class	RserveRExecutor	This class define a RServe RExecutor.

Methods in fr.ens.biologie.genomique.eoulsan.util.r that return RExecutor

Modifier and Type	Method	Description
static RExecutor	RExecutorFactory.newRExecutor(RExecutorFactory.Mode mode, String rServeServer, String dockerImage, File outputDirectory, File temporaryDirectory)	Create a new instance of RExecutor.