colocalisation
gentropy.colocalisation.ColocalisationStep
¶
Colocalisation step.
This workflow runs colocalisation analyses that assess the degree to which independent signals of the association share the same causal variant in a region of the genome, typically limited by linkage disequilibrium (LD).
Source code in src/gentropy/colocalisation.py
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__init__(session: Session, credible_set_path: str, coloc_path: str, colocalisation_method: str, colocalisation_method_params: dict[str, Any] | None = None) -> None
¶
Run Colocalisation step.
This step allows for running two colocalisation methods: ecaviar and coloc.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
session
|
Session
|
Session object. |
required |
credible_set_path
|
str
|
Input credible sets path. |
required |
coloc_path
|
str
|
Output path. |
required |
colocalisation_method
|
str
|
Colocalisation method. |
required |
colocalisation_method_params
|
dict[str, Any] | None
|
Keyword arguments passed to the colocalise method of Colocalisation class. Defaults to None |
None
|
Other Parameters:
Name | Type | Description |
---|---|---|
priorc1 |
float
|
Prior on variant being causal for trait 1. Defaults to 1e-4. For coloc method only. |
priorc2 |
float
|
Prior on variant being causal for trait 2. Defaults to 1e-4. For coloc method only. |
priorc12 |
float
|
Prior on variant being causal for both traits. Defaults to 1e-5. For coloc method only. |
overlap_size_cutoff |
int
|
Minimum number of overlapping variants bfore filtering. Defaults to 0. |
posterior_cutoff |
float
|
Minimum overlapping Posterior probability cutoff for small overlaps. Defaults to 0.0. |
Source code in src/gentropy/colocalisation.py
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