Uses of Class ubic.gemma.rest.util.args.GeneArg (Gemma 1.31.13 API)

Packages that use GeneArg
Package Description

ubic.gemma.rest

ubic.gemma.rest.util.args

Uses of GeneArg in ubic.gemma.rest

Methods in ubic.gemma.rest with parameters of type GeneArg
Modifier and Type	Method	Description
`Object`	DatasetsWebService.`getDatasetsDifferentialExpressionAnalysisResultsForGene(GeneArg<?> geneArg, QueryArg query, FilterArg<ExpressionExperiment> filter, OffsetArg offsetArg, LimitArg limitArg, Double threshold, javax.ws.rs.core.HttpHeaders headers)`	Obtain differential expression analysis results for a given gene.
`Object`	DatasetsWebService.`getDatasetsDifferentialExpressionAnalysisResultsForGeneInTaxon(TaxonArg<?> taxonArg, GeneArg<?> geneArg, QueryArg query, FilterArg<ExpressionExperiment> filter, OffsetArg offsetArg, LimitArg limitArg, Double threshold, javax.ws.rs.core.HttpHeaders headers)`	Obtain differential expression analysis results for a given gene in a given taxon.
`PaginatedResponseDataObject<ExperimentExpressionLevelsValueObject>`	DatasetsWebService.`getDatasetsExpressionLevelsForGene(GeneArg<?> geneArg, QueryArg queryArg, FilterArg<ExpressionExperiment> filterArg, OffsetArg offsetArg, LimitArg limitArg, Boolean keepNonSpecific, ExpLevelConsolidationArg consolidate)`	Retrieve the expression levels of a given gene across all datasets.
`PaginatedResponseDataObject<ExperimentExpressionLevelsValueObject>`	DatasetsWebService.`getDatasetsExpressionLevelsForGeneInTaxon(TaxonArg<?> taxonArg, GeneArg<?> geneArg, QueryArg queryArg, FilterArg<ExpressionExperiment> filterArg, OffsetArg offsetArg, LimitArg limitArg, Boolean keepNonSpecific, ExpLevelConsolidationArg consolidate)`	Retrieve the expression levels of a given gene and taxon across all datasets.
`ResponseDataObject<List<GeneEvidenceValueObject>>`	GeneWebService.`getGeneEvidence(GeneArg<?> geneArg)`	Deprecated.
`ResponseDataObject<List<CoexpressionValueObjectExt>>`	GeneWebService.`getGeneGeneCoexpression(GeneArg<?> geneArg, GeneArg<?> with, LimitArg limit, Integer stringency)`	Retrieves the coexpression of two given genes.
`ResponseDataObject<List<GeneOntologyTermValueObject>>`	GeneWebService.`getGeneGoTerms(GeneArg<?> geneArg)`	Retrieves the GO terms of the given gene.
`ResponseDataObject<List<PhysicalLocationValueObject>>`	GeneWebService.`getGeneLocations(GeneArg<?> geneArg)`	Retrieves the physical location of the given gene.
`PaginatedResponseDataObject<CompositeSequenceValueObject>`	GeneWebService.`getGeneProbes(GeneArg<?> geneArg, OffsetArg offset, LimitArg limit)`	Retrieves the probes (composite sequences) with this gene.
`ResponseDataObject<List<GeneEvidenceValueObject>>`	TaxaWebService.`getGenesEvidenceInTaxon(TaxonArg<?> taxonArg, GeneArg<?> geneArg)`	Deprecated.
`ResponseDataObject<List<GeneOntologyTermValueObject>>`	TaxaWebService.`getTaxonGeneGoTerms(TaxonArg<?> taxonArg, GeneArg<?> geneArg)`
`ResponseDataObject<List<PhysicalLocationValueObject>>`	TaxaWebService.`getTaxonGeneLocations(TaxonArg<?> taxonArg, GeneArg<?> geneArg)`	Retrieves gene location for the gene on the given taxon.
`PaginatedResponseDataObject<CompositeSequenceValueObject>`	TaxaWebService.`getTaxonGeneProbes(TaxonArg<?> taxonArg, GeneArg<?> geneArg, OffsetArg offsetArg, LimitArg limitArg)`

Uses of GeneArg in ubic.gemma.rest.util.args

Subclasses of GeneArg in ubic.gemma.rest.util.args
Modifier and Type	Class	Description
`class`	`GeneEnsemblIdArg`	Long argument type for Gene API, referencing the Gene Ensembl ID.
`class`	`GeneNcbiIdArg`	Long argument type for Gene API, referencing the Gene NCBI ID.
`class`	`GeneSymbolArg`	String argument type for Gene API.

Methods in ubic.gemma.rest.util.args that return GeneArg
Modifier and Type	Method	Description
`static GeneArg<?>`	GeneArg.`valueOf(String s)`	Used by RS to parse value of request parameters.

Methods in ubic.gemma.rest.util.args with parameters of type GeneArg
Modifier and Type	Method	Description
`List<Gene>`	GeneArgService.`getEntitiesWithTaxon(GeneArg<?> genes, Taxon taxon)`	Obtain genes from a specific taxon.
`Gene`	GeneArgService.`getEntityWithTaxon(GeneArg<?> entityArg, Taxon taxon)`	Obtain a gene from a specific taxon.
`List<GeneEvidenceValueObject>`	GeneArgService.`getGeneEvidence(GeneArg<?> arg, Taxon taxon)`	Deprecated.
`List<GeneOntologyTermValueObject>`	GeneArgService.`getGeneGoTerms(GeneArg<?> arg)`	Returns GO terms for the gene that this GeneArg represents.
`List<GeneOntologyTermValueObject>`	GeneArgService.`getGeneGoTermsInTaxon(GeneArg<?> geneArg, Taxon taxon)`	Obtain GO terms for the gene in the given taxon.
`List<PhysicalLocationValueObject>`	GeneArgService.`getGeneLocation(GeneArg<?> geneArg)`	Returns all known locations of the gene(s) that this GeneArg represents.
`List<PhysicalLocationValueObject>`	GeneArgService.`getGeneLocationInTaxon(GeneArg<?> arg, Taxon taxon)`	Returns all known locations of the gene that this GeneArg represents.
`Slice<CompositeSequenceValueObject>`	GeneArgService.`getGeneProbes(GeneArg<?> geneArg, int offset, int limit)`	Obtain probes for the gene across all platforms.
`Slice<CompositeSequenceValueObject>`	GeneArgService.`getGeneProbesInTaxon(GeneArg<?> geneArg, Taxon taxon, int offset, int limit)`	Obtain probes for the gene in the given taxon across all platforms.