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qlu-lab / PUMAS

Fine-tuning polygenic risk score models using GWAS summary statistics
MIT License
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Naming patterns and minor QoL issues #13

Open melothemightyone opened 1 year ago

melothemightyone commented 1 year ago

Just my 2cents: PUMAS is a great innovative tool. However, IMO, a very minor issue with PUMAS is the inconsistent and convoluted naming pattern between subsampling and eval function. More specifically, subsampling.R supports the ``--chr'' flag and eval.R doesn't. I had to go through the code to manually fix this.

Another issue is that loading the entire LD block file is extremly time-consuming and memory-consuming. Why not break them down by chromosome?

I think the authors could fix this should they ever decide to update PUMAS.

qlu-lab commented 1 year ago

Hi Zichen,

Thank you for the comments and I appreciate the feedback! We will address both points you made in our next update soon.

Zijie