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mecfs_bio.analysis.decode_me_initial_analysis

Script to run initial analysis on DecodeME data.

Functions:

run_initial_decode_me_analysis 

run_initial_decode_me_analysis()

Function to run initial analysis on DecodeME data.

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
  • USe of Mendelian Randomization to look for causal blood proteins

Comment out lines to remove tasks

Source code in mecfs_bio/analysis/decode_me_initial_analysis.py 
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def run_initial_decode_me_analysis():
    """
    Function to run initial analysis on DecodeME data.

    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
    - USe of Mendelian Randomization to look for causal blood proteins


    Comment out lines to remove tasks
    """
    DEFAULT_RUNNER.run(
        [
            DECODE_ME_GWAS_1_MANHATTAN_AND_QQ_PLOT,
            DECODE_ME_GWAS_1_MANHATTAN_PLOT,
            DECODE_ME_GWAS_1_LEAD_VARIANTS,
            MAGMA_DECODE_ME_SPECIFIC_TISSUE_ANALYSIS_BAR_PLOT,
            DECODE_ME_MASTER_GENE_LIST_AS_MARKDOWN,
        ]
        + DECODE_ME_S_LDSC.get_terminal_tasks()
        + DECODE_ME_HBA_MAGMA_TASKS.terminal_tasks(),
        # + DECODE_ME_BASIC_CIS_PQTL_MR.terminal_tasks(),
        incremental_save=True,
        must_rebuild_transitive=[
            DECODE_ME_GWAS_1_37_ANNOVAR_DBSNP150_RSID_ASSIGNED.harmonize_task
        ],
    )