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mecfs_bio.analysis.syncope

Analyze the syncope GWAS of Aegisdottir et al.

Functions:

run_syncope_analysis 

run_syncope_analysis()

Analyze GWAS of syncope from Aegisdottir et al. Includes: - MAGMA using GTEx bulk RNAseq reference data - MAGMA using human brain atlas single cell RNAseq reference data - S-LDSC using standard reference datasets.

Source code in mecfs_bio/analysis/syncope.py 
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def run_syncope_analysis():
    """
    Analyze GWAS of syncope from Aegisdottir et al.
    Includes:
    - MAGMA using GTEx bulk RNAseq reference data
    - MAGMA using human brain atlas single cell RNAseq reference data
    - S-LDSC using standard reference datasets.
    """
    DEFAULT_RUNNER.run(
        [
            AEGISDOTTIR_ET_AL_RAW_SYNCOPE_DATA,
        ]
        + SYNCOPE_S_LDSC_TASKS.get_terminal_tasks()
        + HBA_MAGMA_AEGISDOTTIR_SYCNOPE_GWAS.terminal_tasks()
        + AEGISDOTTIR_COMBINED_MAGMA_TASKS.inner.terminal_tasks(),
        incremental_save=True,
        must_rebuild_transitive=[AEGISDOTTIR_COMBINED_MAGMA_TASKS.sumstats_task],
    )