Skip to content

mecfs_bio.analysis.schizophrenia_analysis

Analyze Schizophrenia dataset from PGC 2022

Functions:

run_initial_schizophrenia_analysis 

run_initial_schizophrenia_analysis()

Function to analyze GWAS of Schizophrenia phenotype. Includes: - S-LDSC analysis - MAGMA analysis (Using both GTEx and HBA reference data)

Source code in mecfs_bio/analysis/schizophrenia_analysis.py 
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
def run_initial_schizophrenia_analysis():
    """
    Function to analyze GWAS of Schizophrenia phenotype.
    Includes:
    - S-LDSC analysis
    - MAGMA analysis (Using both GTEx and HBA reference data)
    """
    DEFAULT_RUNNER.run(
        [
            # PGC_2022_SCH_RAW,
            # PGC2022_SCH_MAGMA_ENTREZ_ANNOTATIONS,
            # PGC2022_SCH_MAGMA_ENTREZ_GENE_ANALYSIS
            # MAGMA_PGC2022_SCH_HUMAN_BRAIN_ATLAS_GENE_COVAR
            # PGC_2022_SCH_MAGMA_HUMAN_BRAIN_ATLAS_PLOT,
            # MAGMA_PGC2022_SCH_HUMAN_BRAIN_ATLAS_CONDITIONAL_ANALYSIS
            # MAGMA_PGC2022_HBA_FORWARD_STEPWISE_CLUSTER_SELECT,
            # PGC2022_HBA_MAGMA_STEPWISE_PLOT
            SCH_PGC_2022_STANDARD_ANALYSIS.hba_magma_tasks.magma_independent_cluster_plot
        ],
        # ]+ SCH_PGC_2022_STANDARD_ANALYSIS.get_terminal_tasks(),
        # must_rebuild_transitive=[PGC2022_SCH_MAGMA_ENTREZ_ANNOTATIONS]
        # must_rebuild_transitive=[PGC2022_HBA_MAGMA_SPEC_MATRIX_FILTERED],
        # must_rebuild_transitive=[
        #     PGC2022_HBA_MAGMA_STEPWISE_PLOT,
        #     MAGMA_PGC2022_HBA_FORWARD_STEPWISE_CLUSTER_SELECT,
        # ],
        must_rebuild_transitive=[
            SCH_PGC_2022_STANDARD_ANALYSIS.hba_magma_tasks.magma_independent_cluster_plot
        ],
    )