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mecfs_bio.analysis.ldl_analysis

Script to run basic analysis of LDL GWAS from the Million Veterans Program.

Functions:

run_ldl_analysis 

run_ldl_analysis() -> None

Apply standard LDL analysis: - Using MAGMA to combine the LDL GWAS summary statistics with tissue-specific expression data from GTEx to identify key tissues involved in control of LDL levels. - Using S-LDSC to identify key tissues and cell types via a heritability model

Source code in mecfs_bio/analysis/ldl_analysis.py 
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def run_ldl_analysis() -> None:
    """
    Apply standard LDL analysis:
    - Using MAGMA to combine the LDL GWAS summary statistics with tissue-specific expression data from GTEx to identify key tissues involved in control of LDL levels.
    - Using S-LDSC to identify key tissues and cell types via a heritability model
    """
    DEFAULT_RUNNER.run(
        [
            MILLION_VETERANS_EUR_LDL_MAGMA_TASKS.inner.bar_plot_task,
            MILLION_VETERANS_EUR_LDL_MAGMA_TASKS.inner.labeled_filtered_gene_analysis_task,
        ]
        + list(LDL_STANDARD_SLDSC_TASK_GROUP.get_terminal_tasks()),
        incremental_save=True,
        must_rebuild_transitive=[
            LDL_STANDARD_SLDSC_TASK_GROUP.partitioned_tasks[
                "multi_tissue_gene_expression"
            ].add_categories_task_unwrap
        ],
    )