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mecfs_bio.assets.gwas.myocardial_infarction.analysis.mi_standard_analysis

Attributes:

MILLION_VETERAN_MI_EUR_STANDARD_ANALYSIS module-attribute 

MILLION_VETERAN_MI_EUR_STANDARD_ANALYSIS = concrete_standard_analysis_generator_assume_already_has_rsid(
    base_name="million_veterans_mi",
    raw_gwas_data_task=MILLION_VETERAN_MI_EUR_DATA_RAW,
    sample_size=432053,
    fmt=GWASLabColumnSpecifiers(
        chrom="chromosome",
        pos="base_pair_location",
        ea="effect_allele",
        nea="other_allele",
        OR="odds_ratio",
        eaf="effect_allele_frequency",
        p="p_value",
        rsid="rsid",
    ),
    include_hba_magma_tasks=True,
    hba_plot_settings=PlotSettings("plotly_white"),
    include_independent_cluster_plot_in_hba=True,
    pre_sldsc_pipe=CompositePipe(
        [ComputeBetaPipe(), ComputeSEPipe()]
    ),
    include_master_gene_lists=False,
    gget_settings=None,
    manhattan_settings=ManhattanPlotSettings(),
    phenotype_info_for_ldsc=BinaryPhenotypeSampleInfo(
        sample_prevalence=0.09,
        estimated_population_prevalence=0.04,
    ),
)