Study Locus Overlap
gentropy.dataset.study_locus_overlap.StudyLocusOverlap
dataclass
¶
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/gentropy/dataset/study_locus_overlap.py
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|
from_associations(study_locus: StudyLocus, study_index: StudyIndex) -> StudyLocusOverlap
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/gentropy/dataset/study_locus_overlap.py
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|
get_schema() -> StructType
classmethod
¶
Provides the schema for the StudyLocusOverlap dataset.
Returns:
Name | Type | Description |
---|---|---|
StructType |
StructType
|
Schema for the StudyLocusOverlap dataset |
Source code in src/gentropy/dataset/study_locus_overlap.py
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Schema¶
root
|-- leftStudyLocusId: long (nullable = false)
|-- rightStudyLocusId: long (nullable = false)
|-- chromosome: string (nullable = true)
|-- tagVariantId: string (nullable = false)
|-- statistics: struct (nullable = true)
| |-- 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_logBF: double (nullable = true)
| |-- right_logBF: double (nullable = true)
| |-- left_posteriorProbability: double (nullable = true)
| |-- right_posteriorProbability: double (nullable = true)