Add Coverage Analysis

[gwaybio]

Here I add a module (a new module 7) for tracking gene set coverage across algorithms, dimensions, and seeds.

I also add an initial bash script that will run all analyses and the first iteration of results

[ajlee21]

Looks good.

Just a clarifying comment as I'm not as familiar with gene enrichment analyses.

So for a given gene set (which are a set of genes that are in the same pathway?) you are looking to determine which z feature contains the most gene sets? I'm a bit confused because if this assumption is true then I think that all the z features contain all genes just weighted differently so how are you looking for a difference between z's?

[gwaybio]

So for a given gene set (which are a set of genes that are in the same pathway?)

Gene sets are groups of genes that correspond to specific biology, which include pathways.

you are looking to determine which z feature contains the most gene sets? I'm a bit confused because if this assumption is true then I think that all the z features contain all genes just weighted differently so how are you looking for a difference between z's?

I am looking to see which gene sets are enriched in the z features. I determine enriched gene sets based on which genes are upweighted and downweighted in the z features. So, I am looking to determine the coverage, or proportion, of the gene set compendium that are captured by the algorithms with a given z dimension. Since I am also building 5 models per dimension, I am also tracking the gene set coverage of these ensemble models.