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mecfs_bio.analysis.ibd_analysis

Script to analyze inflammatory bowel disease GWAS from Liu et al.

Functions:

  • run_ibd_analysis –

    This script runs a basic analysis of the IBD GWAS from Liu et al.

run_ibd_analysis 

run_ibd_analysis()

This script runs a basic analysis of the IBD GWAS from Liu et al. It includes:

  • Using MAGMA to combine the IBD GWAS summary statistics with tissue-specific expression data from GTEx to identify possible tissues involved in the IBD disease process.
  • S-LDSC analysis using standard reference data
Source code in mecfs_bio/analysis/ibd_analysis.py 
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def run_ibd_analysis():
    """
    This script runs a basic analysis of the IBD GWAS from Liu et al.
    It includes:


    - Using MAGMA to combine the IBD GWAS summary statistics with tissue-specific expression data from GTEx to identify possible tissues involved in the IBD disease process.
    - S-LDSC analysis using standard reference data
    """
    DEFAULT_RUNNER.run(
        [
            LIU_ET_AL_IBD_EUR_37_SPECIFIC_TISSUE_ANALYSIS_BAR_PLOT,
        ]
        + IBD_HBA_MAGMA_TASKS.terminal_tasks(),
        # + LIU_ET_AL_S_LSDC_FROM_SNP_150.get_terminal_tasks(),
        incremental_save=True,
        must_rebuild_transitive=[IBD_HBA_MAGMA_TASKS.magma_independent_cluster_plot],
    )