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Study Locus Overlap

Schema

root
 |-- leftStudyLocusId: long (nullable = false)
 |-- rightStudyLocusId: long (nullable = false)
 |-- chromosome: string (nullable = false)
 |-- tagVariantId: string (nullable = false)
 |-- statistics: struct (nullable = false)
 |    |-- left_pValueMantissa: float (nullable = true)
 |    |-- left_pValueExponent: integer (nullable = true)
 |    |-- right_pValueMantissa: float (nullable = true)
 |    |-- right_pValueExponent: integer (nullable = true)
 |    |-- left_beta: double (nullable = true)
 |    |-- right_beta: double (nullable = true)
 |    |-- left_logABF: double (nullable = true)
 |    |-- right_logABF: double (nullable = true)
 |    |-- left_posteriorProbability: double (nullable = true)
 |    |-- right_posteriorProbability: double (nullable = true)

API

Bases: Dataset

Study-Locus overlap.

This dataset captures pairs of overlapping StudyLocus: that is associations whose credible sets share at least one tagging variant.

Note

This is a helpful dataset for other downstream analyses, such as colocalisation. This dataset will contain the overlapping signals between studyLocus associations once they have been clumped and fine-mapped.

Source code in src/otg/dataset/study_locus_overlap.py 
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@dataclass
class StudyLocusOverlap(Dataset):
    """Study-Locus overlap.

    This dataset captures pairs of overlapping `StudyLocus`: that is associations whose credible sets share at least one tagging variant.

    !!! note
        This is a helpful dataset for other downstream analyses, such as colocalisation. This dataset will contain the overlapping signals between studyLocus associations once they have been clumped and fine-mapped.
    """

    @classmethod
    def get_schema(cls: type[StudyLocusOverlap]) -> StructType:
        """Provides the schema for the StudyLocusOverlap dataset."""
        return parse_spark_schema("study_locus_overlap.json")

    @classmethod
    def from_associations(
        cls: type[StudyLocusOverlap], study_locus: StudyLocus, study_index: StudyIndex
    ) -> StudyLocusOverlap:
        """Find the overlapping signals in a particular set of associations (StudyLocus dataset).

        Args:
            study_locus (StudyLocus): Study-locus associations to find the overlapping signals
            study_index (StudyIndex): Study index to find the overlapping signals

        Returns:
            StudyLocusOverlap: Study-locus overlap dataset
        """
        return study_locus.find_overlaps(study_index)

from_associations(study_locus, study_index) classmethod

Find the overlapping signals in a particular set of associations (StudyLocus dataset).

Parameters:

Name Type Description Default
study_locus StudyLocus

Study-locus associations to find the overlapping signals

 required
study_index StudyIndex

Study index to find the overlapping signals

 required

Returns:

Name Type Description
StudyLocusOverlap StudyLocusOverlap

Study-locus overlap dataset
Source code in src/otg/dataset/study_locus_overlap.py 
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@classmethod
def from_associations(
    cls: type[StudyLocusOverlap], study_locus: StudyLocus, study_index: StudyIndex
) -> StudyLocusOverlap:
    """Find the overlapping signals in a particular set of associations (StudyLocus dataset).

    Args:
        study_locus (StudyLocus): Study-locus associations to find the overlapping signals
        study_index (StudyIndex): Study index to find the overlapping signals

    Returns:
        StudyLocusOverlap: Study-locus overlap dataset
    """
    return study_locus.find_overlaps(study_index)

get_schema() classmethod

Provides the schema for the StudyLocusOverlap dataset.

Source code in src/otg/dataset/study_locus_overlap.py 
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@classmethod
def get_schema(cls: type[StudyLocusOverlap]) -> StructType:
    """Provides the schema for the StudyLocusOverlap dataset."""
    return parse_spark_schema("study_locus_overlap.json")
  • 2023-01-20
  • 2023-08-22
  • Contributors
    • ireneisdoomed
    • d0choa