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omerwe / polyfun

PolyFun (POLYgenic FUNctionally-informed fine-mapping)
MIT License
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Pipeline for summary based prediction. (PolyPredR) #65

Closed zhilizheng closed 3 years ago

zhilizheng commented 3 years ago

Hi,

I only get the summary data, and can't find the steps to run the PolyPredR.

  1. Could I use the linear regression results in the finemapping steps (instead of BOLT results)?
  2. How to input the output from SBayesR or PRSCS results for tagging effect?

Thanks.

omerwe commented 3 years ago

Hi,

Please simply specify the output files containing the beta coefficients in the --betas argument (just like you can do it with BOLT-LMM, you can also do it with LDPred, PRS-CS, etc.). However, you will have to concatenate the per-chromosome files into a single file that contains all the SNPs across all the chromosomes.

If you run into any issues, please let me know!