MTAG allele frequency

[fmurgia]

Hi,

I'm looking at the MTAG output file (tutorial_results_1.1NS_trait_1.txt) and I'm wondering how allele frequencies are estimated (rs2736372 , freq = 0.4179).

I suspect that MTAG reports the allele frequencies of trait 1 and does not estimate the allele frequencies of the combined traits.

Can you enlighten me on this?

Regards,

Federico

[paturley]

If I recall correctly, MTAG reports an N-weighted average of the allele frequencies across the summary stats. Can you confirm, Jon?

On Wed, Aug 23, 2023, 6:24 AM Federico Murgia @.***> wrote:

Hi,

I'm looking at the MTAG output file (tutorial_results_1.1NS_trait_1.txt) and I'm wondering how allele frequencies are estimated (freq = 0.4179).

I suspect that MTAG reports the allele frequencies of trait 1 and does not estimate the allele frequencies of the combined traits.

Can you enlighten me on this?

Regards,

Federico

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[JonJala]

This is not code that I actually wrote myself, and trying to trace through it myself in the code, it's a bit convoluted, so I'm not entirely certain. You could try just passing trait 1 through by itself and see if the number stays the same?

On Wed, Aug 23, 2023 at 7:26 AM paturley @.***> wrote:

If I recall correctly, MTAG reports an N-weighted average of the allele frequencies across the summary stats. Can you confirm, Jon?

On Wed, Aug 23, 2023, 6:24 AM Federico Murgia @.***> wrote:

Hi,

I'm looking at the MTAG output file (tutorial_results_1.1NS_trait_1.txt) and I'm wondering how allele frequencies are estimated (freq = 0.4179).

I suspect that MTAG reports the allele frequencies of trait 1 and does not estimate the allele frequencies of the combined traits.

Can you enlighten me on this?

Regards,

Federico

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