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JonJala / mtag

Python command line tool for Multi-Trait Analysis of GWAS (MTAG)
GNU General Public License v3.0
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std_betas and perfect_gencov #98

Open jianvhuang opened 4 years ago

jianvhuang commented 4 years ago

I am running MTAG with multiple measures of the same traits. GWAS are from the same samples. I used beta and se as input. It seems that I cannot call std_betas and perfect_gencov simultaneously.

I wonder why this is the case? And in when is std_betas recommended?

Thank you

paturley commented 4 years ago

Honestly, I'm not sure why a person would want to use the std-betas option. MTAG by default uses Z-statistics to do its analysis, which means the results are in standardized units, which are then transformed into allele count units before they are returned. That option just skips the last step. We included it just for the flexibility.

On Sat, Jul 4, 2020 at 2:49 PM jianhuang notifications@github.com wrote:

I am running MTAG with multiple measures of the same traits. GWAS are from the same samples. I used beta and se as input. It seems that I cannot call std_betas and perfect_gencov simultaneously.

I wonder why this is the case? And in when is std_betas recommended?

Thank you

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jianvhuang commented 4 years ago

Thank you for clarifying.