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mecfs_bio.analysis.lee_educational_attainment_analysis

Script to run initial analysis on Lee et al. Educational Attainment GWAS

Functions:

  • run_edu_analysis –

    Function to run initial analysis on the Lee et al. Educational Attainment GWAS

run_edu_analysis 

run_edu_analysis()

Function to run initial analysis on the Lee et al. Educational Attainment GWAS Includes:

  • Calculating heritability by LDSC
  • Plotting key tissues as determined by MAGMA Gene Level Analysis of key cells and tissues of SLDSC
  • Use S-LSDC to look for key tissues and cells using standard reference datasets
Source code in mecfs_bio/analysis/lee_educational_attainment_analysis.py 
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def run_edu_analysis():
    """
    Function to run initial analysis on the Lee et al. Educational Attainment GWAS
    Includes:

    - Calculating heritability by LDSC
    - Plotting key tissues as determined by MAGMA Gene Level Analysis of key cells and tissues of SLDSC
    - Use S-LSDC to look for key tissues and cells using standard reference datasets

    """
    DEFAULT_RUNNER.run(
        [
            LEE_ET_AL_2018_COMBINED_MAGMA_TASKS.inner.bar_plot_task,
            # LEE_ET_AL_2018_H2_BY_LDSC,
        ]
        + LEE_ET_AL_2018_HBA_MAGMA_TASKS_EDU.terminal_tasks(),
        +LEE_ET_AL_EDU_STANDARD_SLDSC_TASK_GROUP.get_terminal_tasks(),
        incremental_save=True,
    )