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@shz9 shz9 released this 08 Jan 05:05
v0.1.2
e6f0790

Changed

  • Fixed bug in implementation of .fit method of VIPRS models. Specifically,
    there was an issue with the continued=True flag not working because the OptimizeResult
    object wasn't refreshed.
  • Replaced print statements with logging where appropriate (still needs some more work).
  • Updated way we measure peak memory in viprs_fit
  • Updated dict_concat to just return the element if there's a single entry.
  • Refactored pars of VIPRS to cache some recurring computations.
  • Updated VIPRSBMA & VIPRSGridSearch to only consider models that
    successfully converged.
  • Fixed bug in psuedo_metrics when extracting summary statistics data.
  • Streamlined evaluation code.
  • Refactored code to slightly reduce import/load time.
  • Fixed bug in viprs_evaluate

Added

  • Added SNP position to output table from VIPRS objects.
  • Added measure of time taken to prepare data in viprs_fit.
  • Added option to keep long-range LD regions in viprs_fit.
  • Added convergence check based on parameter values.
  • Added min_iter parameter to .fit methods to ensure CAVI is run for at least min_iter iterations.
  • Added separate method for initializing optimization-related objects.
  • Added regularization penalty lambda_min.
  • Added Spearman R and residualized R-Squared metrics to continuous metrics.

Additional files

Attached are LD matrices for 6 continental ancestry groups, as defined by the Pan-UKB project. The LD matrices are estimated from unrelated samples in the UK Biobank using block-diagonal masks.

Assets 8
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