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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 –

    This script runs a basic analysis of the LDL GWAS from the Million Veterans Program

run_ldl_analysis 

run_ldl_analysis()

This script runs a basic analysis of the LDL GWAS from the Million Veterans Program

This includes:

  • 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():
    """
    This script runs a basic analysis of the LDL GWAS from the Million Veterans Program

    This includes:

    - 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,
        ]
        + 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
        ],
    )