Class DifferentialExpressionAnalysisTaskCommand

java.lang.Object
ubic.gemma.core.job.TaskCommand
ubic.gemma.core.tasks.analysis.diffex.DifferentialExpressionAnalysisTaskCommand
All Implemented Interfaces:
Serializable
Direct Known Subclasses:
DifferentialExpressionAnalysisRemoveTaskCommand
public class DifferentialExpressionAnalysisTaskCommand extends TaskCommand
A command object to be used by spaces.
Author:
keshav
See Also:

  • Constructor Details

  • Method Details

    • getTaskClass

      public Class<? extends Task<? extends TaskCommand>> getTaskClass()
      Description copied from class: TaskCommand
      Obtain the class of the Task object that will be run for this command.

      If null, the task command cannot be submitted through TaskRunningService.submitTaskCommand(TaskCommand) and a task object must be explicitly created.

      For now, this how we map from TaskCommand to Task that actually runs it. We have to have this mapping somewhere until we make Tasks themselves serializable. Tasks are not readily serializable because they have dependencies to Spring services. at which point TaskCommand can be deprecated(or remain as TaskContext).

      Overrides:
      getTaskClass in class TaskCommand

    • getAnalysisType

      public AnalysisType getAnalysisType()
      Proposed analysis type. If null the system tries to figure it out.

    • getExpressionExperiment

      public ExpressionExperiment getExpressionExperiment()

    • getFactors

      public Collection<ExperimentalFactor> getFactors()
      The factors to actually use in the analysis. If null the system tries to figure it out.

    • isForceAnalysis

      public boolean isForceAnalysis()

    • isIncludeInteractions

      public boolean isIncludeInteractions()
      Whether interactions among the factors should be included. The implementation may limit this to two-way interactions for only up to two factors, so this may not have the effect desired.

    • isModerateStatistics

      public boolean isModerateStatistics()
      Whether to moderate test statistics via empirical Bayes

    • getSubsetFactor

      public ExperimentalFactor getSubsetFactor()

    • getToRedo

      public DifferentialExpressionAnalysis getToRedo()

    • isUseWeights

      public boolean isUseWeights()
      Whether to use weighted regression based on mean-variance relationships (voom)

    • setAnalysisType

      public void setAnalysisType(AnalysisType analysisType)
      Proposed analysis type. If null the system tries to figure it out.

    • setExpressionExperiment

      public void setExpressionExperiment(ExpressionExperiment expressionExperiment)

    • setFactors

      public void setFactors(Collection<ExperimentalFactor> factors)
      The factors to actually use in the analysis. If null the system tries to figure it out.

    • setForceAnalysis

      public void setForceAnalysis(boolean forceAnalysis)

    • setIncludeInteractions

      public void setIncludeInteractions(boolean includeInteractions)
      Whether interactions among the factors should be included. The implementation may limit this to two-way interactions for only up to two factors, so this may not have the effect desired.

    • setModerateStatistics

      public void setModerateStatistics(boolean moderateStatistics)
      Whether to moderate test statistics via empirical Bayes

    • setSubsetFactor

      public void setSubsetFactor(ExperimentalFactor subsetFactor)

    • setToRedo

      public void setToRedo(DifferentialExpressionAnalysis toRedo)

    • setUseWeights

      public void setUseWeights(boolean useWeights)
      Whether to use weighted regression based on mean-variance relationships (voom)