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stephenslab / ldshrink

ldshrink: a one-stop R package for shrinkage estimation of linkage disequilibrium
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Allow people to use a faster `cov()` #5

Closed xiangzhu closed 6 years ago

xiangzhu commented 6 years ago

https://github.com/stephenslab/LDshrink/blob/a8fdff30a4df3b202a9932aeb9aa4d3debc7d535/R/LDshrink.R#L10

Here the cov() seems to be the default one in R, but Nick also has a faster cov() based on C (which does not handle NA well though). We should allow people to use this faster one, if they wish and can provide input data without NA.

CreRecombinase commented 6 years ago

with the latest commit, specifying na.rm=F now causes the faster cov routine to be used