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junyangq / snpnet

snpnet: Fast and scalable lasso/elastic-net solver for large SNP data
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Can snpnet be used on bed files directly? #34

Closed privefl closed 3 years ago

privefl commented 4 years ago

I think the preprint says that snpnet can be used on bed files directly. However, the documentation seems to talk only about pgen files.

Could you please clarify this point?

junyangq commented 4 years ago

Hi @privefl thanks for raising this point. In the latest version of the manuscript, we assume pgen files, to be consistent with the latest version of the package. To use bed files, one may need to use an earlier version of the package as in branch V1.0.

privefl commented 4 years ago

Thanks for your reply. In the latest version of the manuscript, you still talk about doing some optimized matrix computations because you have only 0s, 1s, 2s and NAs. Are you still using this when using pgen files? Do you handle dosage data?

privefl commented 4 years ago

Moreover, you still talk about

Moreover, the existing convenient data interface provided by the BEDMatrix package further facilitates our implementation.

whereas BEDMatrix does not handle pgen format yet, but only bed format for now, if I'm not mistaken.

junyangq commented 4 years ago

Good catches. I take back the previous reply and sorry for the confusion. In fact the description and results in the paper should be all about the earlier version of the package https://github.com/junyangq/snpnet/tree/V1.0. We will correct the pgen assumption in the paper and add discussion about major changes and further optimizations made for the latest implementation.

junyangq commented 4 years ago

Thank you @privefl for pointing out this issue!

privefl commented 4 years ago

Could I ask how far is it from being published?

junyangq commented 4 years ago

It's under review after a major revision.