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mecfs_bio.analysis.bmi_analysis

Script to analyze the GIANT + UK Biobank GWAS of body mass index from Pulit et al.

Functions:

  • run_bmi_analysis –

    Apply the standard analysis pipeline to the BMI GWAS of Pulit et al. (2019).

run_bmi_analysis 

run_bmi_analysis() -> None

Apply the standard analysis pipeline to the BMI GWAS of Pulit et al. (2019). Analysis includes: - Application of MAGMA to GTEx data to identify possible key tissues. - Application of MAGMA to human brain atlas to identify key brain tissue - Use of S-LDSC to investigate key cell and tissue types - Estimation of SNP heritability via LDSC

Source code in mecfs_bio/analysis/bmi_analysis.py 
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def run_bmi_analysis() -> None:
    """
    Apply the standard analysis pipeline to the BMI GWAS of Pulit et al. (2019).
    Analysis includes:
    - Application of MAGMA to GTEx data to identify possible key tissues.
    - Application of MAGMA to human brain atlas to identify key brain tissue
    - Use of S-LDSC to investigate key cell and tissue types
    - Estimation of SNP heritability via LDSC
    """
    DEFAULT_RUNNER.run(
        PULIT_ET_AL_2018_BMI_STANDARD_ANALYSIS.get_terminal_tasks(),
        incremental_save=True,
        must_rebuild_transitive=[],
    )