Perform `colSums(X^2)` on FBM object

privefl / bigstatsr

R package for statistical tools with big matrices stored on disk.

https://privefl.github.io/bigstatsr/

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Perform `colSums(X^2)` on FBM object #166

Closed fmorgante closed 1 year ago

fmorgante commented 1 year ago

Hi Florian, I need to do colSums(X^2) where X is an FBM object. Do you have any suggestion on how to do that using bigstatsr functions? I don't seem to find an efficient way.

privefl commented 1 year ago

Hi, I can see 3 ways:

either using big_apply() to simply do it in base R by block (look at the examples)
in Rcpp if you know a bit of C++
with big_colstats(), using var(X) = E(X^2) - E(X)^2

fmorgante commented 1 year ago

The third point is a great trick I did not think about. Thank you!