Package ubic.gemma.core.loader.expression.ucsc.cellbrowser

Class UcscCellBrowserUtils

java.lang.Object

ubic.gemma.core.loader.expression.ucsc.cellbrowser.UcscCellBrowserUtils

public class UcscCellBrowserUtils
extends Object

Author:

poirigui

Constructor Summary

Constructors

Constructor	Description
UcscCellBrowserUtils()

Method Summary

Modifier and Type	Method	Description
static Dataset	getDataset(String datasetId)
static SingleCellExpressionDataMatrix<?>	getDatasetDataMatrix(String datasetId, QuantitationType quantitationType, Map<String,CompositeSequence> designElementsMap, Map<String,BioAssay> cellIdToAssayMap, ProgressReporter progressReporter)	Create a stream over the expression data matrix of a given dataset.
static DatasetDescription	getDatasetDescription(String datasetId)
static Map<String,Map<String,Object>>	getDatasetMetadata(String datasetId)	Retrieve the metadata for a given dataset.
static Map<String,Object>	getDatasetMetadata(String datasetId, String metaField)	Retrieve the metadata for a specific field.
static List<DatasetSummary>	getDatasets()	Obtain all the UCSC Cell Browser datasets.
static String	getDatasetUri(String datasetId)	Construct a URL to access an UCSC Cell Browser dataset.

Methods inherited from class java.lang.Object

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

Constructor Details

UcscCellBrowserUtils

public UcscCellBrowserUtils()

Method Details

getDatasets

public static List<DatasetSummary> getDatasets()
                                        throws IOException

Obtain all the UCSC Cell Browser datasets.

Throws:

IOException

getDataset

public static Dataset getDataset(String datasetId)
                          throws IOException

Throws:

IOException

getDatasetDescription

public static DatasetDescription getDatasetDescription(String datasetId)
                                                throws IOException

Throws:

IOException

getDatasetUri

public static String getDatasetUri(String datasetId)

Construct a URL to access an UCSC Cell Browser dataset.

getDatasetMetadata

public static Map<String,Map<String,Object>> getDatasetMetadata(String datasetId)
                                                         throws IOException

Retrieve the metadata for a given dataset.

Returns:

a mapping of cell IDs to their metadata fields.

Throws:

IOException

getDatasetMetadata

public static Map<String,Object> getDatasetMetadata(String datasetId,
 String metaField)
                                             throws IOException

Retrieve the metadata for a specific field.

Returns:

a mapping of cell IDs to the value of the specified metadata field.

Throws:

IOException

getDatasetDataMatrix

public static SingleCellExpressionDataMatrix<?> getDatasetDataMatrix(String datasetId,
 QuantitationType quantitationType,
 Map<String,CompositeSequence> designElementsMap,
 Map<String,BioAssay> cellIdToAssayMap,
 ProgressReporter progressReporter)
                                                              throws IOException

Create a stream over the expression data matrix of a given dataset.

Parameters:

designElementsMap -

cellIdToAssayMap - mapping of cell IDs to BioAssay they belong to

Throws:

IOException