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JonJala
Due to bugs in the beta-se code, this option has been temporarily removed from the MTAG software
How can I address the following error?
File "mtag.py", line 1546, in
That error will be thrown when trying to use the beta-se option (there are bugs in that code we haven't been able to track down), so if you refrain from using that option, you should be ok and won't see that error.
On Tue, Mar 22, 2022, 2:21 PM Mahantesh Biradar @.***> wrote:
How can I address the following error?
File "mtag.py", line 1546, in raise RuntimeError("Due to bugs in the beta-se code, this option has been temporarily removed from the MTAG software. Dec 2, 2021") RuntimeError: Due to bugs in the beta-se code, this option has been temporarily removed from the MTAG software. Dec 2, 2021
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We recently noticed something that looked like a software bug in the beta-SE option, so we flipped it off until we can look into it. For now, you'll need to use the default Z-N option, which requires a z-stat and sample size.
On Tue, Mar 22, 2022, 2:21 PM Mahantesh Biradar @.***> wrote:
How can I address the following error?
File "mtag.py", line 1546, in raise RuntimeError("Due to bugs in the beta-se code, this option has been temporarily removed from the MTAG software. Dec 2, 2021") RuntimeError: Due to bugs in the beta-se code, this option has been temporarily removed from the MTAG software. Dec 2, 2021
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I wanted to use this function because I only have BETA & SE in sum stats. Any workaround?
You can calculate Z using Z = beta/SE and I bet the N is reported in the associated paper if you looked it up.
Best, Patrick
On Tue, Mar 22, 2022 at 2:48 PM Mahantesh Biradar @.***> wrote:
I wanted to use this function because I only have BETA & SE in sum stats. Any workaround?
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Dear developers,
I was wondering if the option use_beta_will be re-enabled for MTAG since when calculating MTAG for binary phenotypes using Z and N, the recalculation of beta and se can be affected by limitations in the effective N calculation, with inappropriate scaling of the beta and se.
Many thanks!
Paloma
Hi Paloma,
Fixing up the beta-se functionality is on our list of things we'd like to do, but like everyone, we are also swamped with other work, so I don't know how soon we will be able to figure out what is wrong.
You should be able to infer how to rescale the betas and SEs if you run MTAG on just the single set of GWAS summary statistics for the binary phenotype. The ratio of the new betas over the old ones should be constant for all SNPs, and if you multiply your full MTAG sumstats by this ratio, I think it will get you back to your original units. (It's worth thinking about whether this is sensible though. I'm just brainstorming and have never tried this.)
Patrick
On Tue, Mar 21, 2023 at 2:41 PM pjordab @.***> wrote:
Dear developers,
I was wondering if the option use_beta_will be re-enabled for MTAG since when calculating MTAG for binary phenotypes using Z and N, the recalculation of beta and se can be affected by limitations in the effective N calculation, with inappropriate scaling of the beta and se.
Many thanks!
Paloma
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