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neurogenomics / MAGMA_Celltyping

Find causal cell-types underlying complex trait genetics
https://neurogenomics.github.io/MAGMA_Celltyping
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`get_driver_genes`: select genes by mean rank #116

Closed bschilder closed 2 years ago

bschilder commented 2 years ago

Determine driver genes by:

  1. Computing the rank based on "ADJ_ZSTAT"
  2. Computing the rank based on "specificity_proportion"
  3. Taking the mean of these two ranks.
  4. Sorting the table by the new column "mean_rank" and selecting the top n_genes

The idea behind this is that the genes that are both heavily influencing GWAS gene scores and CTD specificity scores will contribute the most to cell-type-specific enrichment.

Previously, get_driver_genes was only selecting genes based on "ADJ_ZSTAT" after filtering by the top specificity decile, but this two-step process used arbitrary cutoffs and didn't quite capture the driver gene idea as well.