mecfs_bio.assets.gwas.me_cfs.decode_me.analysis.magma

Tasks analyzing DecodeME data using MAGMA

Modules:

• decode_me_curated_gene_set_analysis –
• decode_me_filtered_gene_list –
• decode_me_filtered_gene_list_with_gene_metadata –

  Add Gene symbols, Entrez IDs, and Gene descriptions to the list of significant genes produced by MAGMA.

• decode_me_filtered_gene_list_with_gene_metadata_drop_cols –

  Keep only the essential columns from the filtered genelist

• decode_me_gwas_1_build_37_entrez_gsea_hallmark_gene_sets –
• decode_me_gwas_1_build_37_magma_ensembl_specific_tissue_gene_sets –
• decode_me_gwas_1_build_37_magma_ensembl_specific_tissue_gene_sets_brain_average –

  Similar to MAGMA_DECODE_ME_SPECIFIC_TISSUE_GENE_SET_ANALYSIS, but averages across brain tissues.

• decode_me_hba_magma_analysis –

  Task generator to analyze decodeME GWAS 1 using the human brian atlas reference dataset

• decode_me_magma_gene_plot –

  This task plots the gene-level p-values produced by MAGMA analysis of DecodeME, using strict

• decode_me_magma_gene_plot_with_window –

  This task plots the gene-level p-values produced by MAGMA analysis of DecodeME,

• magma_specific_tissue_bar_plot –
• magma_specific_tissue_bar_plot_brain_average –

  Analogous to MAGMA_DECODE_ME_SPECIFIC_TISSUE_ANALYSIS_BAR_PLOT, but controls for average across brain tissue, not all tissues.