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pcarbo / varbvs

Large-scale Bayesian variable selection for R and MATLAB.
http://pcarbo.github.io/varbvs
GNU General Public License v3.0
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Is it better to use PIP or Bayes factor for variable selection? #43

Open garyzhubc opened 1 week ago

garyzhubc commented 1 week ago

Is it better to use PIP or Bayes factor for variable selection? I saw that the paper gives the option of computing Bayes factor of some null models. Would PIP or the Bayes factor give better result of finding which SNP is causal?

pcarbo commented 1 week ago

@garyzhubc I would not recommend using varbvs for identifying causal SNPs; for this, you should use susieR.

garyzhubc commented 1 week ago

Hi Dr Carbonetto, Thanks for the feedback. Could you please explain why?

pcarbo commented 1 week ago

@garyzhubc Please see the susie paper or, for a shorter explanation, see Sec. 3.5.7 of the mr.ash paper.