ubic.gemma.persistence.service.expression.experiment

Interface GeeqService

All Superinterfaces:

BaseReadOnlyService<Geeq>, BaseService<Geeq>, BaseVoEnabledService<Geeq,GeeqValueObject>

All Known Implementing Classes:

GeeqServiceImpl

public interface GeeqService
extends BaseVoEnabledService<Geeq,GeeqValueObject>

Nested Class Summary

Nested Classes

Modifier and Type	Interface and Description
static class	GeeqService.ScoreMode Modes for filling GEEQ scores.

Method Summary

Modifier and Type	Method and Description
Geeq	calculateScore(ExpressionExperiment ee, GeeqService.ScoreMode mode) Calculates the GEEQ score in the given mode for the experiment with the given id.
void	setManualOverrides(ExpressionExperiment ee, GeeqAdminValueObject gqVo) Reads manual override info from the given GEEQ Value Object and stores them with the experiment

Methods inherited from interface ubic.gemma.persistence.service.BaseVoEnabledService

loadAllValueObjects, loadValueObject, loadValueObjectById, loadValueObjects, loadValueObjectsByIds

Methods inherited from interface ubic.gemma.persistence.service.BaseService

create, create, findOrCreate, remove, remove, remove, removeAllInBatch, save, save, update, update

Methods inherited from interface ubic.gemma.persistence.service.BaseReadOnlyService.BaseReadOnlyService

countAll, find, findOrFail, load, load, loadAll, loadOrFail

Method Detail

calculateScore

Geeq calculateScore(ExpressionExperiment ee,
                    GeeqService.ScoreMode mode)

Calculates the GEEQ score in the given mode for the experiment with the given id.

Parameters:

eeId - the id of the experiment to calculate the scores for.

mode - either run all scores, or only re-score batch effect, batch confound or replicates.

setManualOverrides

void setManualOverrides(ExpressionExperiment ee,
                        GeeqAdminValueObject gqVo)

Reads manual override info from the given GEEQ Value Object and stores them with the experiment

Parameters:

eeId - the id of the experiment to update the geeq information for.

gqVo - a GEEQ Value Object containing the necessary information.