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mecfs_bio.analysis.finngen_r13_migraine_analysis

Script to perform standard analysis on the FinnGen release 13 GWAS of migraine and its subtypes.

Functions:

run_finngen_r13_migraine_analysis 

run_finngen_r13_migraine_analysis() -> None

Function to perform standard analysis on the FinnGen R13 migraine endpoints: G6_MIGRAINE, MIGRAINE_TRIPTAN, G6_MIGRAINE_NO_AURA, and G6_MIGRAINE_WITH_AURA.

Includes S-LDSC, LDSC heritability, GTEx MAGMA, HBA MAGMA, H-MAGMA, gene set analysis, lead variant extraction, and Manhattan plots.

Source code in mecfs_bio/analysis/finngen_r13_migraine_analysis.py 
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def run_finngen_r13_migraine_analysis() -> None:
    """
    Function to perform standard analysis on the FinnGen R13 migraine endpoints:
    G6_MIGRAINE, MIGRAINE_TRIPTAN, G6_MIGRAINE_NO_AURA, and G6_MIGRAINE_WITH_AURA.

    Includes S-LDSC, LDSC heritability, GTEx MAGMA, HBA MAGMA, H-MAGMA, gene set analysis,
    lead variant extraction, and Manhattan plots.
    """
    DEFAULT_RUNNER.run(
        FINNGEN_R13_MIGRAINE_STANDARD_ANALYSIS.get_terminal_tasks()
        + FINNGEN_R13_MIGRAINE_TRIPTAN_STANDARD_ANALYSIS.get_terminal_tasks()
        + FINNGEN_R13_MIGRAINE_NO_AURA_STANDARD_ANALYSIS.get_terminal_tasks()
        + FINNGEN_R13_MIGRAINE_WITH_AURA_STANDARD_ANALYSIS.get_terminal_tasks(),
        incremental_save=True,
        must_rebuild_transitive=[],
    )