Uses of Class
ubic.gemma.core.loader.expression.geo.model.GeoSample

Packages that use GeoSample

Package	Description
ubic.gemma.core.loader.expression.geo
ubic.gemma.core.loader.expression.geo.model
ubic.gemma.core.loader.expression.geo.singleCell	This package contains specific logic for dealing with single-cell data from GEO.

Uses of GeoSample in ubic.gemma.core.loader.expression.geo

Methods in ubic.gemma.core.loader.expression.geo that return types with arguments of type GeoSample

Modifier and Type	Method	Description
static Map<GeoPlatform,List<GeoSample>>	DatasetCombiner.getPlatformSampleMap(GeoSeries geoSeries)
Map<String,GeoSample>	GeoParseResult.getSampleMap()
Map<String,GeoSample>	GeoParseResult.getSamples()

Uses of GeoSample in ubic.gemma.core.loader.expression.geo.model

Methods in ubic.gemma.core.loader.expression.geo.model that return types with arguments of type GeoSample

Modifier and Type	Method	Description
Collection<GeoSample>	GeoReplication.getSamples()
Collection<GeoSample>	GeoSeries.getSamples()
Collection<GeoSample>	GeoSubset.getSamples()
Collection<GeoSample>	GeoVariable.getSamples()

Methods in ubic.gemma.core.loader.expression.geo.model with parameters of type GeoSample

Modifier and Type	Method	Description
void	GeoSeries.addSample(GeoSample sample)
void	GeoSubset.addSample(GeoSample sample)
void	GeoValues.addSample(GeoSample sample)	Only call this to add a sample for which there are no data.
void	GeoReplication.addToRepeatsSampleList(GeoSample sample)
void	GeoVariable.addToVariableSampleList(GeoSample sample)
void	GeoValues.addValue(GeoSample sample, Integer quantitationTypeIndex, String designElement, String value)	Store a value.

Method parameters in ubic.gemma.core.loader.expression.geo.model with type arguments of type GeoSample

Modifier and Type	Method	Description
void	GeoSeries.addSamples(Collection<GeoSample> s)	Add a group of samples to this series.
void	GeoValues.clear(GeoPlatform platform, List<GeoSample> datasetSamples, Integer quantitationTypeIndex)	If possible, null out the data for a quantitation type on a given platform.
Integer[]	GeoValues.getIndices(GeoPlatform platform, List<GeoSample> neededSamples, Integer quantitationType)	Get the indices of the data for a set of samples - this can be used to get a slice of the data.
GeoValues	GeoSeries.getValues(Collection<GeoSample> s)	Get a subset of the values.
void	GeoSeries.keepSamples(Collection<GeoSample> samplesToKeep)	Only keep the given samples.
void	GeoSeries.removeSamples(Collection<GeoSample> samplesToSkip)	Clean up samples we have decided are ineligible (i.e., non transcriptomic)
void	GeoReplication.setSamples(Collection<GeoSample> repeatsSampleList)
void	GeoVariable.setSamples(Collection<GeoSample> variableSampleList)
GeoValues	GeoValues.subset(Collection<GeoSample> samples)	This creates a new GeoValues that has data only for the selected samples.

Uses of GeoSample in ubic.gemma.core.loader.expression.geo.singleCell

Methods in ubic.gemma.core.loader.expression.geo.singleCell with parameters of type GeoSample

Modifier and Type	Method	Description
Path	AbstractSingleFileInSeriesSingleCellDetector.downloadSingleCellData(GeoSample sample)
Path	GeoSingleCellDetector.downloadSingleCellData(GeoSample sample)
Path	GeoSingleCellDetector.downloadSingleCellData(GeoSample sample, SingleCellDataType dataType)
Path	GeoSingleCellDetector.downloadSingleCellData(GeoSeries series, GeoSample sample)	Download a sample in the context of a series.
Path	GeoSingleCellDetector.downloadSingleCellData(GeoSeries series, GeoSample sample, SingleCellDataType dataType)
Path	MexDetector.downloadSingleCellData(GeoSample sample)	Retrieve single-cell data for the given GEO sample to disk.
Path	MexDetector.downloadSingleCellData(GeoSeries series, GeoSample sample)	Download a GEO sample within the context of its series.
Path	SeriesAwareSingleCellDetector.downloadSingleCellData(GeoSeries series, GeoSample sample)
Path	SingleCellDetector.downloadSingleCellData(GeoSample sample)	Download single-cell data for the given GEO sample.
List<String>	AbstractSingleFileInSeriesSingleCellDetector.getAdditionalSupplementaryFiles(GeoSample sample)
List<String>	GeoSingleCellDetector.getAdditionalSupplementaryFiles(GeoSample sample)
List<String>	GeoSingleCellDetector.getAdditionalSupplementaryFiles(GeoSeries series, GeoSample sample)
List<String>	MexDetector.getAdditionalSupplementaryFiles(GeoSample sample)
List<String>	MexDetector.getAdditionalSupplementaryFiles(GeoSeries series, GeoSample sample)
List<String>	SeriesAwareSingleCellDetector.getAdditionalSupplementaryFiles(GeoSeries series, GeoSample sample)
List<String>	SingleCellDetector.getAdditionalSupplementaryFiles(GeoSample sample)	Obtain a list of all additional supplementary files.
boolean	AbstractSingleFileInSeriesSingleCellDetector.hasSingleCellData(GeoSample sample)	Detection is not supported at the sample level.
boolean	GeoSingleCellDetector.hasSingleCellData(GeoSample sample)
boolean	GeoSingleCellDetector.hasSingleCellData(GeoSeries series, GeoSample sample)
boolean	LoomSingleCellDetector.hasSingleCellData(GeoSample sample)
boolean	MexDetector.hasSingleCellData(GeoSample sample)
boolean	MexDetector.hasSingleCellData(GeoSample sample, boolean allowArchiveLookup)	Check if a GEO sample contains single-cell data.
boolean	MexDetector.hasSingleCellData(GeoSeries series, GeoSample sample)	Check if a sample contains single-cell data in the context of its series.
boolean	SeriesAwareSingleCellDetector.hasSingleCellData(GeoSeries series, GeoSample sample)
boolean	SingleCellDetector.hasSingleCellData(GeoSample sample)	Indicate if the given GEO sample has single cell data.
boolean	GeoSingleCellDetector.hasSingleCellDataInSra(GeoSample sample)	Check if a GEO sample has single-cell data in SRA.
boolean	GeoSingleCellDetector.isSingleCell(GeoSample sample, boolean hasSingleCellDataInSeries)	Check if a GEO sample is single-cell by looking up its metadata.
boolean	GeoSingleCellDetector.isSingleNuclei(GeoSample sample, boolean hasSingleCellDataInSeries)	Check if a GEO sample is single-nuclei by looking up its metadata.