Package ubic.gemma.web.controller.diff

Class DifferentialExpressionSearchController

java.lang.Object

ubic.gemma.web.controller.diff.DifferentialExpressionSearchController

@Controller
public class DifferentialExpressionSearchController
extends Object

A controller used to get differential expression analysis and meta analysis results.

Author:

keshav

Constructor Summary

Constructors

Constructor	Description
DifferentialExpressionSearchController()

Method Summary

Modifier and Type	Method	Description
Collection<ubic.gemma.model.analysis.expression.diff.DifferentialExpressionValueObject>	getDifferentialExpression(Long geneId, double threshold)	AJAX entry which returns results on a non-meta analysis basis.
Collection<ubic.gemma.model.analysis.expression.diff.DifferentialExpressionValueObject>	getDifferentialExpression(Long geneId, double threshold, Integer limit)	AJAX entry which returns results on a non-meta analysis basis.
Collection<ubic.gemma.model.analysis.expression.diff.DifferentialExpressionValueObject>	getDifferentialExpressionWithoutBatch(Long geneId, double threshold, Integer limit)	AJAX entry which returns results on a non-meta analysis basis.
Collection<ExpressionExperimentExperimentalFactorValueObject>	getFactors(Collection<Long> eeIds)	AJAX entry.
String	scheduleDiffExpSearchTask(Long taxonId, ubic.gemma.model.expression.experiment.ExpressionExperimentSetValueObject eevo, ubic.gemma.model.genome.gene.GeneSetValueObject gsvo)	AJAX - method used for main display metaheatmap.

Methods inherited from class java.lang.Object

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

Constructor Detail

DifferentialExpressionSearchController

public DifferentialExpressionSearchController()

Method Detail

getDifferentialExpression

public Collection<ubic.gemma.model.analysis.expression.diff.DifferentialExpressionValueObject> getDifferentialExpression(Long geneId,
                                                                                                                         double threshold)

AJAX entry which returns results on a non-meta analysis basis. That is, the differential expression results for the gene with the id, geneId, are returned.

getDifferentialExpression

public Collection<ubic.gemma.model.analysis.expression.diff.DifferentialExpressionValueObject> getDifferentialExpression(Long geneId,
                                                                                                                         double threshold,
                                                                                                                         Integer limit)

AJAX entry which returns results on a non-meta analysis basis. That is, the differential expression results for the gene with the id, geneId, are returned.

getDifferentialExpressionWithoutBatch

public Collection<ubic.gemma.model.analysis.expression.diff.DifferentialExpressionValueObject> getDifferentialExpressionWithoutBatch(Long geneId,
                                                                                                                                     double threshold,
                                                                                                                                     Integer limit)

AJAX entry which returns results on a non-meta analysis basis. That is, the differential expression results for the gene with the id, geneId, are returned. This method is just like getDifferentialExpression but any analyses with the 'batch' factor are filtered out because they are not biologically relevant

getFactors

public Collection<ExpressionExperimentExperimentalFactorValueObject> getFactors(Collection<Long> eeIds)

AJAX entry. Value objects returned contain experiments that have 2 factors and have had the diff analysis run on it.

scheduleDiffExpSearchTask

public String scheduleDiffExpSearchTask(Long taxonId,
                                        ubic.gemma.model.expression.experiment.ExpressionExperimentSetValueObject eevo,
                                        ubic.gemma.model.genome.gene.GeneSetValueObject gsvo)

AJAX - method used for main display metaheatmap.