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variani / finemapr

Fine-mapping pipeline in R: FINEMAP, CAVIAR, PAINTOR, GCTA-COJO, ABF
GNU General Public License v3.0
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Number of causal SNPs #12

Closed daria-nikanorova closed 3 years ago

daria-nikanorova commented 3 years ago

Hello and thank you for your tool!

Could you please explain, how the number of causal SNPs for FINEMAP is chosen in your implementation?

variani commented 3 years ago

Hi,

Your question is more related to the FINEMAP method itself rather than my package. When I was running FINEMAP, the default value for the maximum number of causal SNPs was 5 (that might be changed in the current version of FINEMAP). Obviously, you can specify a number >5.

Again, I would suggest to run FINEMAP directly and avoid using my package because I've stopped using/maintaining it.

Best, Andrey