Package ubic.gemma.core.loader.expression

Interface DataLoader

All Superinterfaces:
AutoCloseable, Closeable
All Known Subinterfaces:
SequencingDataLoader, SingleCellDataLoader
All Known Implementing Classes:
AbstractDelegatingDataLoader, AbstractDelegatingSequencingDataLoader, AbstractDelegatingSingleCellDataLoader, AnnDataSingleCellDataLoader, GenericMetadataSingleCellDataLoader, MexSingleCellDataLoader, NullSingleCellDataLoader, SequencingMetadataFileDataLoader, SequencingMetadataFileSingleCellDataLoader
public interface DataLoader extends Closeable
Base interface for loading expression data in Gemma.
Author:
poirigui

  • Method Details

    • setBioAssayToSampleNameMapper

      void setBioAssayToSampleNameMapper(BioAssayMapper bioAssayToSampleNameMatcher)
      Set the strategy used for mapping BioAssay to sample names from the data.

    • setIgnoreUnmatchedSamples

      void setIgnoreUnmatchedSamples(boolean ignoreUnmatchedSamples)
      Ignore unmatched samples from the data.

      This defaults to true.

    • setDesignElementToGeneMapper

      void setDesignElementToGeneMapper(DesignElementMapper designElementToGeneMapper)
      Set the strategy used for mapping CompositeSequence to gene identifiers from the data.

    • setIgnoreUnmatchedDesignElements

      void setIgnoreUnmatchedDesignElements(boolean ignoreUnmatchedDesignElements)
      Ignore unmatched design elements from the data when creating vectors.

      This defaults to true.

      There's a discussions to make this default in false in general for sequencing data.

    • getSampleNames

      Set<String> getSampleNames() throws IOException
      Obtain the sample names present in the data.
      Throws:
      IOException

    • getQuantitationTypes

      Set<QuantitationType> getQuantitationTypes() throws IOException
      Load quantitation types present in the data.
      Throws:
      IOException

    • getFactors

      Set<ExperimentalFactor> getFactors(Collection<BioAssay> samples, @Nullable Map<BioMaterial,Set<FactorValue>> factorValueAssignments) throws IOException
      Load experimental factors present in the data.
      Parameters:
      samples - samples to use when determining which factors to load
      factorValueAssignments - if non-null, the proposed assignment of factor values to samples are populated in the mapping.
      Returns:
      a set of factors present in the data
      Throws:
      IOException

    • getSamplesCharacteristics

      Map<BioMaterial,Set<Characteristic>> getSamplesCharacteristics(Collection<BioAssay> samples) throws IOException
      Load samples characteristics present in the data.
      Parameters:
      samples - to use when determining which characteristics to load
      Returns:
      proposed characteristics grouped by sample
      Throws:
      IOException

    • getGenes

      Set<String> getGenes() throws IOException
      Load gene identifiers present in the data.
      Throws:
      IOException

    • close

      void close() throws IOException
      Free any resources that the loaded has setup.
      Specified by:
      close in interface AutoCloseable
      Specified by:
      close in interface Closeable
      Throws:
      IOException