Jonathan Jala

You could try making use of the median_z_cutoff flag to relax the threshold on that check: https://github.com/JonJala/mtag/blob/master/mtag.py#L1540C4-L1540C4 On Wed, Oct 25, 2023 at 9:11 AM caozilongsupper ***@***.***> wrote: > Thanks...

Do you mind including the whole log? It might help to see what came before. On Thu, Oct 26, 2023 at 5:14 AM caozilongsupper ***@***.***> wrote: > Hi JonJala, >...

Hmm, it's unclear what's going on there. Have you switched all your files to be whitespace-delimited? And there is a "snpid" column in each? On Sat, Oct 28, 2023 at...

What does your invocation of MTAG look like? (As in what parameters are you passing?). It looks like you're passing in an 'n' when it expects a number, based on...

I'm sorry, but I don't understand what you mean. What data and what link?

Are you sure you filtered out all the "AGAAGA" SNPs? It looks like there are perhaps still some in your sample based on that error message.

Hmm, it looks like it's possibly one of the FRQ columns, based on the line that's throwing the error (mtag.py line 357 it looks like ). If you are willing...

I'm not sure what the differences are between Python and R in terms of how they read things in and convert to numeric values. R is apparently making some judgment...

Hi, It's on the list of things to do, but probably not going to happen in the near future, unfortunately. On Thu, Jul 25, 2024 at 3:09 PM Kori Clermont...

It looks like you're running into issues in the sumstats.py file. If you make changes [here](https://github.com/JonJala/mtag/blob/9e17f3cf1fbcf57b6bc466daefdc51fd0de3c5dc/ldsc_mod/ldscore/sumstats.py#L152) and [here](https://github.com/JonJala/mtag/blob/9e17f3cf1fbcf57b6bc466daefdc51fd0de3c5dc/ldsc_mod/ldscore/sumstats.py#L24) , changing the 22 to 18, that might help unstick you? It's...