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JonJala / mtag

Python command line tool for Multi-Trait Analysis of GWAS (MTAG)
GNU General Public License v3.0
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Can the MTAG results be used for a meta-analysis? #203

Open zhuyanchen116 opened 7 months ago

zhuyanchen116 commented 7 months ago

For example, we analyzed 3 GWAS statistics from different ancestries (EUR, EAS, AFR), and produced 3 MTAG results. Can we perform a cross-ancestry meta-analysis for these MTAG results?

paturley commented 7 months ago

I'm confused by your question. You are using MTAG within an ancestry across several traits and then you'd like to meta-analyze with a trait across ancestries?

On Wed, Jan 3, 2024 at 8:26 AM zhuyanchen116 @.***> wrote:

For example, we analyzed 3 GWAS statistics from different ancestries (EUR, EAS, AFR), and produced 3 MTAG results. Can we perform a cross-ancestry meta-analysis for these MTAG results?

— Reply to this email directly, view it on GitHub https://github.com/JonJala/mtag/issues/203, or unsubscribe https://github.com/notifications/unsubscribe-auth/AFBUB5KJVLHNHOMPZ2QJEADYMVL7TAVCNFSM6AAAAABBLNZLGOVHI2DSMVQWIX3LMV43ASLTON2WKOZSGA3DIMBTGY3DOOI . You are receiving this because you are subscribed to this thread.Message ID: @.***>

zhuyanchen116 commented 7 months ago

Thank you for your reply. For example, 1.we used MTAG within 2 traits (trait1 and trait2) from EUR. 2.we used MTAG within 2 traits (trait1 and trait2) from AFR. 3.we used MTAG within 2 traits (trait1 and trait2) from EAS. The above analyses generated trait1_MTAG_EUR, trait1_MTAG_EAS, and trait1_MTAG_AFR. Lastly, we would like to perform a cross-ancestry meta-analysis within trait1_MTAG_EUR, trait1_MTAG_EAS, and trait1_MTAG_AFR.

paturley commented 7 months ago

This sounds reasonable to me. I can't think of why you shouldn't be able to do this (though sometimes I'm not creative enough to anticipate problems that I haven't tested...)

On Wed, Jan 3, 2024 at 10:17 PM zhuyanchen116 @.***> wrote:

Thank you for your reply. For example, 1.we used MTAG within 2 traits (trait1 and trait2) from EUR. 2.we used MTAG within 2 traits (trait1 and trait2) from AFR. 3.we used MTAG within 2 traits (trait1 and trait2) from EAS. The above analyses generated trait1_MTAG_EUR, trait1_MTAG_EAS, and trait1_MTAG_AFR. Lastly, we would like to perform a cross-ancestry meta-analysis within trait1_MTAG_EUR, trait1_MTAG_EAS, and trait1_MTAG_AFR.

— Reply to this email directly, view it on GitHub https://github.com/JonJala/mtag/issues/203#issuecomment-1876253541, or unsubscribe https://github.com/notifications/unsubscribe-auth/AFBUB5MXRQVERLILYCPAWMDYMYNNLAVCNFSM6AAAAABBLNZLGOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQNZWGI2TGNJUGE . You are receiving this because you commented.Message ID: @.***>