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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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class WindowBasedClumpingStep:
    """Apply window based clumping on summary statistics datasets."""

    def __init__(
        self,
        session: Session,
        summary_statistics_input_path: str,
        study_locus_output_path: str,
        distance: int = WindowBasedClumpingStepConfig().distance,
        gwas_significance: float = WindowBasedClumpingStepConfig().gwas_significance,
        collect_locus: bool = WindowBasedClumpingStepConfig().collect_locus,
        collect_locus_distance: int = WindowBasedClumpingStepConfig().collect_locus_distance,
        inclusion_list_path: str
        | None = WindowBasedClumpingStepConfig().inclusion_list_path,
    ) -> None:
        """Run window-based clumping step.

        Args:
            session (Session): Session object.
            summary_statistics_input_path (str): Path to the harmonized summary statistics dataset.
            study_locus_output_path (str): Output path for the resulting study locus dataset.
            distance (int): Distance, within which tagging variants are collected around the semi-index. Optional.
            gwas_significance (float): GWAS significance threshold. Defaults to 5e-8.
            collect_locus (bool): Whether to collect locus around semi-indices. Optional.
            collect_locus_distance (int): Distance, within which tagging variants are collected around the semi-index. Optional.
            inclusion_list_path (str | None): Path to the inclusion list (list of white-listed study identifier). Optional.

        Check WindowBasedClumpingStepConfig object for default values.
        """
        # If inclusion list path is provided, only these studies will be read:
        if inclusion_list_path:
            study_ids_to_ingest = [
                f'{summary_statistics_input_path}/{row["studyId"]}.parquet'
                for row in session.spark.read.parquet(inclusion_list_path).collect()
            ]
        else:
            # If no inclusion list is provided, read all summary stats in folder:
            study_ids_to_ingest = [summary_statistics_input_path]

        ss = SummaryStatistics.from_parquet(
            session,
            study_ids_to_ingest,
            recursiveFileLookup=True,
        )

        # Clumping:
        study_locus = ss.window_based_clumping(
            distance=distance, gwas_significance=gwas_significance
        )

        # Optional locus collection:
        if collect_locus:
            # Collecting locus around semi-indices:
            study_locus = study_locus.annotate_locus_statistics(
                ss, collect_locus_distance=collect_locus_distance
            )

        study_locus.df.write.mode(session.write_mode).parquet(study_locus_output_path)

__init__(session: Session, summary_statistics_input_path: str, study_locus_output_path: str, distance: int = WindowBasedClumpingStepConfig().distance, gwas_significance: float = WindowBasedClumpingStepConfig().gwas_significance, collect_locus: bool = WindowBasedClumpingStepConfig().collect_locus, collect_locus_distance: int = WindowBasedClumpingStepConfig().collect_locus_distance, inclusion_list_path: str | None = WindowBasedClumpingStepConfig().inclusion_list_path) -> 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.

 distance
gwas_significance float

GWAS significance threshold. Defaults to 5e-8.

 gwas_significance
collect_locus bool

Whether to collect locus around semi-indices. Optional.

 collect_locus
collect_locus_distance int

Distance, within which tagging variants are collected around the semi-index. Optional.

 collect_locus_distance
inclusion_list_path str | None

Path to the inclusion list (list of white-listed study identifier). Optional.

 inclusion_list_path

Check WindowBasedClumpingStepConfig object for default values.

Source code in src/gentropy/window_based_clumping.py 
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def __init__(
    self,
    session: Session,
    summary_statistics_input_path: str,
    study_locus_output_path: str,
    distance: int = WindowBasedClumpingStepConfig().distance,
    gwas_significance: float = WindowBasedClumpingStepConfig().gwas_significance,
    collect_locus: bool = WindowBasedClumpingStepConfig().collect_locus,
    collect_locus_distance: int = WindowBasedClumpingStepConfig().collect_locus_distance,
    inclusion_list_path: str
    | None = WindowBasedClumpingStepConfig().inclusion_list_path,
) -> None:
    """Run window-based clumping step.

    Args:
        session (Session): Session object.
        summary_statistics_input_path (str): Path to the harmonized summary statistics dataset.
        study_locus_output_path (str): Output path for the resulting study locus dataset.
        distance (int): Distance, within which tagging variants are collected around the semi-index. Optional.
        gwas_significance (float): GWAS significance threshold. Defaults to 5e-8.
        collect_locus (bool): Whether to collect locus around semi-indices. Optional.
        collect_locus_distance (int): Distance, within which tagging variants are collected around the semi-index. Optional.
        inclusion_list_path (str | None): Path to the inclusion list (list of white-listed study identifier). Optional.

    Check WindowBasedClumpingStepConfig object for default values.
    """
    # If inclusion list path is provided, only these studies will be read:
    if inclusion_list_path:
        study_ids_to_ingest = [
            f'{summary_statistics_input_path}/{row["studyId"]}.parquet'
            for row in session.spark.read.parquet(inclusion_list_path).collect()
        ]
    else:
        # If no inclusion list is provided, read all summary stats in folder:
        study_ids_to_ingest = [summary_statistics_input_path]

    ss = SummaryStatistics.from_parquet(
        session,
        study_ids_to_ingest,
        recursiveFileLookup=True,
    )

    # Clumping:
    study_locus = ss.window_based_clumping(
        distance=distance, gwas_significance=gwas_significance
    )

    # Optional locus collection:
    if collect_locus:
        # Collecting locus around semi-indices:
        study_locus = study_locus.annotate_locus_statistics(
            ss, collect_locus_distance=collect_locus_distance
        )

    study_locus.df.write.mode(session.write_mode).parquet(study_locus_output_path)
  • 2024-01-10
  • 2024-01-18
  • Contributors