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chrchang / plink-ng

A comprehensive update to the PLINK association analysis toolset. Beta testing of the first new version (1.90), focused on speed and memory efficiency improvements, is finishing up. Development is now focused on building out support for multiallelic, phased, and dosage data in PLINK 2.0.

Home Page:https://www.cog-genomics.org/plink/2.0/

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Plans to get pgenlibr on CRAN?

richelbilderbeek opened this issue · comments

commented

Dear @chrchang,

I was happy to find the pgenlibr R package to read .pgen files and I intend to use it in one of my packages.

The problem is that I intend to get my package on CRAN, where CRAN packages are only allowed to depend on CRAN packages.

Are there plans to get the pgenlibr R package on CRAN?

I would be open to help in a way, e.g. by adopting it in my package, but a standalone pgenlibr R package feels preferred to me, especially as -as far as I understand- the .pgen file format is not cast in stone yet.

Thanks for your reply and cheers, Richel Bilderbeek

commented

Yes, there's technically one part of the .pgen format that has not been fleshed out yet (multiallelic dosages), but that part is unimportant for most applications. I will work on it this weekend.

commented

@chrchang that would be amazing! Thanks so much!

commented

Ended up being delayed by far more than a weekend, but pgenlibr is now on CRAN.