How to calculate MDS information (or PCA)

[wei110110]

Dear Liu Lab Thank you for developing this outstanding software and providing it to use. I believe this will contribute significantly to the advancement of TWAS Additionally, it may be extremely useful for me, as my research focuses on non-European populations.

However, I have some questions during the process. How was the PCA information generated (such as af.pca and af.pca.eqtl) ?

I understand that you have described the principles in the paper. What I'm asking is "the software and the general process used". Could you please offer me some suggestions? I would greatly appreciate it.

Wei

[dajiangliu]

Hi, Wei,

I think you can create a matrix of genome-wide allele frequencies and calculate the PCA using R function eigen. We only focus on variants that are shared between different studies. Hope this helps. Thank you!

Thanks, Dajiang

On Wed, Sep 20, 2023 at 10:19 PM wei110110 @.***> wrote:

Thank you for developing this outstanding software and providing it to use. I believe this will contribute significantly to the advancement of TWAS Additionally, it may be extremely useful for me, as my research focuses on non-European populations.

However, I have some questions during the process. How was the PCA information generated (such as af.pca and af.pca.eqtl) ?

I understand that you have described the principles in the paper. What I'm asking is "the software and the general process used". Could you please offer me some suggestions? I would greatly appreciate it.

Wei

— Reply to this email directly, view it on GitHub https://github.com/dajiangliu/rareGWAMA/issues/2, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACNCDJPSQMKNKTHAI7QLKG3X3OP2NANCNFSM6AAAAAA5AZUMHM . You are receiving this because you are subscribed to this thread.Message ID: @.***>

[wei110110]

I am very grateful for the prompt and clear response. I will do my best to try !