Sex encoding might be wrong on documentation

[audreylk]

Hi there,
I have been formatting my local input data as detailed on https://bio-learn.github.io/methylation-standard.html#standard-metadata-fields, which says that the column 'Sex' should be 0 for female and 1 for male. However, when I get my results for GrimAgeV1, it includes a column for Female, which appears to be a copy of the 'Sex' column, meaning that it is showing Female == 0 for those that should actually be female. When I compared the results to results I got from the dnamage online calculator (from the Clock foundation), the results from BioLearn parsed out males and females completely separately (to me, indicating that there was something off about the 2 groups). When I swapped the 'Sex' values that I input in BioLearn and again compared to the Clock Foundation calculator, I found that this time, I got a nice (almost) 1:1 relationship, with males and females mixed together. So I think there might be a mistake in the requested encoding for 'Sex'.

On a side note, the formatting documentation says to have the columns in the metadata as 'Sex' and 'Age', but the functions apparently look for 'sex' and 'age'.

Cheers,
Audrey

[audreylk]

Here's a visualization of what I mean by the males and females parsing out separately...
First, with 'sex' coded the way it states in the documentation (female == 0, male == 1), compared to results from the clock foundation calculator:

And second, with 'sex' coding swapped, so that female == 1 and male == 1, again compared to the results from the clock foundation calculator:

[sarudak]

Thanks for digging into this. We will investigate. If you get a chance can you verify that you have the same behavior with the most recent release?