LD Index

gentropy.dataset.ld_index.LDIndex dataclass

Bases: Dataset

Dataset containing linkage disequilibrium information between variants.

Source code in src/gentropy/dataset/ld_index.py

@dataclass
class LDIndex(Dataset):
    """Dataset containing linkage disequilibrium information between variants."""

    @classmethod
    def get_schema(cls: type[LDIndex]) -> StructType:
        """Provides the schema for the LDIndex dataset.

        Returns:
            StructType: Schema for the LDIndex dataset
        """
        return parse_spark_schema("ld_index.json")

get_schema() -> StructType classmethod

Provides the schema for the LDIndex dataset.

Returns:

Name	Type	Description
StructType	StructType	Schema for the LDIndex dataset

Source code in src/gentropy/dataset/ld_index.py

@classmethod
def get_schema(cls: type[LDIndex]) -> StructType:
    """Provides the schema for the LDIndex dataset.

    Returns:
        StructType: Schema for the LDIndex dataset
    """
    return parse_spark_schema("ld_index.json")

Schema

root
 |-- variantId: string (nullable = false)
 |-- chromosome: string (nullable = false)
 |-- ldSet: array (nullable = false)
 |    |-- element: struct (containsNull = false)
 |    |    |-- tagVariantId: string (nullable = false)
 |    |    |-- rValues: array (nullable = false)
 |    |    |    |-- element: struct (containsNull = false)
 |    |    |    |    |-- population: string (nullable = false)
 |    |    |    |    |-- r: double (nullable = false)

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• 2023-02-27
• 2024-01-17
• Contributors
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