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Speed up processing of large genotype matrices #35

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DavisBrian opened this issue Dec 18, 2017 · 0 comments

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DavisBrian commented Dec 18, 2017

Processing large genotypes take way too long.

It turns out that splitting the matix into genes takes the most time. Probably should change to data.table and possible feather for the backend.

http://kbroman.org/blog/2017/04/30/sqlite-feather-and-fst/

https://stackoverflow.com/questions/39670743/is-there-a-faster-way-to-subset-a-sparse-matrix-than?noredirect=1#comment66739254_39670743

and probably sparse matrix support.

This may break backwards compatibility. seqMeta2 package?

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