Skip to content

mecfs_bio.analysis.asthma

Script to analyze asthma phenotype.

Functions:

run_initial_asthma_analysis 

run_initial_asthma_analysis()

Function to analyze asthma phenotype Includes: - MAGMA and S-LDSC analysis

Source code in mecfs_bio/analysis/asthma.py 
 8
 9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
def run_initial_asthma_analysis():
    """
    Function to analyze asthma phenotype
    Includes:
    - MAGMA and S-LDSC analysis
    """
    DEFAULT_RUNNER.run(
        [
            # ASTHMA_PP_CIS_MR_UNIPROT_LABELED,
            # ASTHMA_HAN_PPP_CIS_MR_MARKDOWN
            # HAN_CIS_PPP_MR_PLOT,
        ],
        # [HAN_2022_ASTHMA_TSMR],
        # [HAN_ET_AL_ASTHMA_RAW] + HAN_ASTHMA_STANDARD_ANALYSIS.get_terminal_tasks(),
        incremental_save=True,
        must_rebuild_transitive=[
            # HAN_CIS_PPP_MR_PLOT
            # ASTHMA_HAN_PPP_CIS_MR_MARKDOWN
            # ASTHMA_PP_CIS_MR_UNIPROT_LABELED
            # HAN_ASTHMA_STANDARD_ANALYSIS.labeled_lead_variant_tasks.raw_sumstats_task
            # HAN_2022_ASTHMA_TSMR
        ],
    )