PICS finemapping of LD-annotated StudyLocus.
Source code in src/gentropy/pics.py
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42 | class PICSStep:
"""PICS finemapping of LD-annotated StudyLocus."""
def __init__(
self,
session: Session,
study_locus_ld_annotated_in: str,
picsed_study_locus_out: str,
) -> None:
"""Run PICS on LD annotated study-locus.
Args:
session (Session): Session object.
study_locus_ld_annotated_in (str): Input LD annotated study-locus path.
picsed_study_locus_out (str): Output PICSed study-locus path.
"""
# Extract
study_locus_ld_annotated = StudyLocus.from_parquet(
session, study_locus_ld_annotated_in
)
# PICS
(
PICS.finemap(study_locus_ld_annotated)
.filter_credible_set(credible_interval=CredibleInterval.IS99)
# Flagging sub-significnat loci:
.validate_lead_pvalue(
pvalue_cutoff=WindowBasedClumpingStepConfig().gwas_significance
)
# Writing the output:
.df.write.mode(session.write_mode)
.parquet(picsed_study_locus_out)
)
|