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mecfs_bio.analysis.million_veterans_cfs_initial_analysis

Functions:

run_initial_mvp_cfs_analysis 

run_initial_mvp_cfs_analysis()

Function to run initial analysis on Million Veterans CFS phenotyp.

Includes:

  • Generation of manhattan plot.
  • Extraction of lead variants.
  • 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
Source code in mecfs_bio/analysis/million_veterans_cfs_initial_analysis.py 
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def run_initial_mvp_cfs_analysis():
    """
    Function to run initial analysis on Million Veterans CFS phenotyp.

    Includes:

    - Generation of manhattan plot.
    - Extraction of lead variants.
    - 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


    """
    DEFAULT_RUNNER.run(
        MILLION_VETERANS_CFS_STANDARD_ANALYSIS_TASK_GROUP.get_terminal_tasks(),
        incremental_save=True,
        must_rebuild_transitive=[],
    )