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Temporary Fix

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@choishingwan choishingwan released this 20 Sep 18:42
· 17 commits to master since this release
2.3.5
9dbf55e

Update Log

This is a temporary fix while we re-structure PRSice for unit testings and improve extensibility. Unfortunately, this fix stretches a rather long period of time, so I might not have an accurate log of changes. Here are what I remembered:

  • Fix --perm. --perm should now run
  • --prevalence should now provide the PRS.R2.adj information correctly
  • We change the calculation of PRS.R2 when covariates were provided. Previous, it was calculated as Full.R2 - Null.R2. Now it is calculated as 1 - ( 1 - Full.R2) / ( 1 - Null.R2)
  • Some slight changes to code such that printing full score matrix should be faster when we have enough memory
  • Some attempt to reduce memory usage for bgen format with mixed success (it still require quite a lot of memory)

Known unfixed issue

  • bgen would not work without --allow-inter
  • bgen require more memory than it should
  • For some reason, we have to manually modify EIGEN library for window compilation. So there might be potential for bugs for the window build.

I will try to fix those whenever I have time, but I will mainly focus on the restructuring of PRSice.

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