mancusolab / geneax

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Implement sparse genotype as linear operator #1

Closed quattro closed 1 year ago

quattro commented 1 year ago

Catch-all for implementing centered/standardized genotypes as a sparse linear operator

quattro commented 1 year ago

This is more or less done, but limited to the BCOO datatype in JaxSparse. Leaving this open for now, if we can extend to BCSR at some point.

quattro commented 1 year ago

Another enhancement would be a "blocked" or "batched" version of this that captures different genotype matrices over different chromosomes. This would have a benefit for downstream solvers by treating the large covariance matrix as block diagonal.