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Benchmark output type

BenchmarkOutputType

Bases: NamedTuple

Represents the structure of benchmark output types.

Attributes:

Name Type Description
prioritisation_type_string str

The type of prioritisation being performed.
y_label str

The label for the y-axis in performance evaluation plots.
columns List[str]

The list of column names relevant to the benchmark output.
result_directory str

The directory where benchmark results are stored.
Source code in src/pheval/analyse/benchmark_output_type.py 
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class BenchmarkOutputType(NamedTuple):
    """
    Represents the structure of benchmark output types.

    Attributes:
        prioritisation_type_string (str): The type of prioritisation being performed.
        y_label (str): The label for the y-axis in performance evaluation plots.
        columns (List[str]): The list of column names relevant to the benchmark output.
        result_directory (str): The directory where benchmark results are stored.
    """

    prioritisation_type_string: str
    y_label: str
    columns: list[str]
    result_directory: str

BenchmarkOutputTypeEnum

Bases: Enum

Enumeration of benchmark output types, representing different entities.

Attributes:

Name Type Description
GENE BenchmarkOutputType

Benchmark output type for gene prioritisation.
VARIANT BenchmarkOutputType

Benchmark output type for variant prioritisation.
DISEASE BenchmarkOutputType

Benchmark output type for disease prioritisation.
Source code in src/pheval/analyse/benchmark_output_type.py 
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class BenchmarkOutputTypeEnum(Enum):
    """
    Enumeration of benchmark output types, representing different entities.

    Attributes:
        GENE (BenchmarkOutputType): Benchmark output type for gene prioritisation.
        VARIANT (BenchmarkOutputType): Benchmark output type for variant prioritisation.
        DISEASE (BenchmarkOutputType): Benchmark output type for disease prioritisation.
    """

    GENE = BenchmarkOutputType(
        "gene",
        "Disease-causing genes (%)",
        ["gene_identifier", "gene_symbol"],
        "pheval_gene_results",
    )
    VARIANT = BenchmarkOutputType("variant", "Disease-causing variants (%)", ["variant_id"], "pheval_variant_results")
    DISEASE = BenchmarkOutputType(
        "disease",
        "Known diseases (%)",
        ["disease_identifier", "mondo_identifier"],
        "pheval_disease_results",
    )