HWE_P in run_eggla_gwas() results inconsistent with analysis plan about eggla HOT 6 CLOSED

Thinking about this, actually, I am not sure if the idea is that eggla package user won't have to edit the summary stats file at all. If the idea is that they check it and do final editing themselves, then maybe it could be clearly stated in the analysis plan. If the idea is that eggla would provide ready to send results, then I think there might be inconsistency also with file delimiter (comma vs tab), and the columns it provides (maybe we'll get to the columns suggested in the analysis plan when we get further with the meta-analysis).

from eggla.

Oh, I missed the part where HWE_P should be NA for imputed variants.
I can fix it.

The goal in my opinion is to make "ready to send" tables, but this does not mean the analysts should not check what they are going to send. They HAVE to check, because they are the only one to have the ability to check if the results is consistent with the data.
Indeed, maybe a "danger" callout fully stating that results check is mandatory can be added in the analytical plan.

from eggla.

@annihei I will fix it soon.

from eggla.

I agree results should always be checked before sending anyway.

from eggla.

@annihei Fix available in v0.18.3

from eggla.

Thank you!

from eggla.