window_based_clumping
gentropy.window_based_clumping.WindowBasedClumpingStep
¶
Apply window based clumping on summary statistics datasets.
Source code in src/gentropy/window_based_clumping.py
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__init__(session: Session, summary_statistics_input_path: str, study_locus_output_path: str, distance: int = 500000, collect_locus: bool = False, collect_locus_distance: int = 500000, inclusion_list_path: str | None = None) -> None
¶
Run window-based clumping step.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
session |
Session
|
Session object. |
required |
summary_statistics_input_path |
str
|
Path to the harmonized summary statistics dataset. |
required |
study_locus_output_path |
str
|
Output path for the resulting study locus dataset. |
required |
distance |
int
|
Distance, within which tagging variants are collected around the semi-index. Optional. |
500000
|
collect_locus |
bool
|
Whether to collect locus around semi-indices. Optional. |
False
|
collect_locus_distance |
int
|
Distance, within which tagging variants are collected around the semi-index. Optional. |
500000
|
inclusion_list_path |
str | None
|
Path to the inclusion list (list of white-listed study identifier). Optional. |
None
|
Source code in src/gentropy/window_based_clumping.py
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