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# skbio.table.example_table

skbio.table.example_table = 2 x 3 <class 'biom.table.Table'> with 5 nonzero entries (83% dense)

  The (canonically pronounced ‘teh’) Table.

  Give in to the power of the Table!

  Creates an in-memory representation of a BIOM file. BIOM version 1.0 is based on JSON to provide the overall structure for the format while versions 2.0 and 2.1 are based on HDF5. For more information see [1] and [2]

  Parameters:
    data array_like

      An (N,M) sample by observation matrix represented as one of these types: * An 1-dimensional array of values * An n-dimensional array of values * An empty list * A list of numpy arrays * A list of dict * A list of sparse matrices * A dictionary of values * A list of lists * A sparse matrix of values

    observation_ids array_like of str

      A (N,) dataset of the observation IDs, where N is the total number of IDs

    sample_ids array_like of str

      A (M,) dataset of the sample IDs, where M is the total number of IDs

    observation_metadata list of dicts, optional

      per observation dictionary of annotations where every key represents a metadata field that contains specific metadata information, ie taxonomy, KEGG pathway, etc

    sample_metadata array_like of dicts, optional

      per sample dictionary of annotations where every key represents a metadata field that contains sample specific metadata information, ie

    table_id str, optional

      A field that can be used to identify the table

    type str, see notes

      The type of table represented

    create_date str, optional

      Date that this table was built

    generated_by str, optional

      Individual who built the table

    observation_group_metadata list, optional

      group that contains observation specific group metadata information (e.g., phylogenetic tree)

    sample_group_metadata list, optional

      group that contains sample specific group metadata information (e.g., relationships between samples)

  Attributes:
    shape
    dtype
    nnz
    matrix_data
    type
    table_id
    create_date
    generated_by
    format_version
  Raises:
    TableException

      When an invalid table type is provided.

  Notes

  Allowed table types are None, “OTU table”, “Pathway table”, “Function table”, “Ortholog table”, “Gene table”, “Metabolite table”, “Taxon table”

  References

  [1]

  http://biom-format.org/documentation/biom_format.html

  [2]

  D. McDonald, et al. “The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome” GigaScience 2012 1:7