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dajiangliu / rareGWAMA

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Confused about the GWAS input of TESLA #3

Open Zenoooo opened 9 months ago

Zenoooo commented 9 months ago

Dear Liu Lab, Hi~, I'm using EAS eQTL data and I don't have ancestry-matched GWAS data. So I want to use TESLA to conduct TWAS analysis, but I'm not sure about the input of the GWAS data. Here are my questions:

  1. Can I use EAS eQTL and a set of Mixed-ancestry GWAS summry data (one summary data including many ancestries) or a set of European ancestry GWAS summary data as input of TESLA?
  2. If could, how should I calculate the MDS information or PCA? I cant only get a AF matrix with 1 rows (GWAS study) and n cols (SNPs).

Thanks Zeno

dajiangliu commented 9 months ago

Hi, Zeno, TESLA works with multiple GWAS datasets potentially from different ancestries. It would be equivalent to standard TWAS method such as PrediXcan, if you only have one set of summary statistics. Hope this helps.

Thanks, Dajiang

Professor & Vice Chair for Research Dept. Public Health Sciences Director, Artificial Intelligence and Biomedical Informatics Co-Chair, Bioinformatics and Genomics Graduate Program Penn State College of Medicine, ASB 4301C Email: @.*** URL: https://dajiangliu.blog https://dajiangliu.blog Tel: +1-717-531-4178

On Sun, Sep 24, 2023 at 11:03 PM Zenoooo @.***> wrote:

Dear Liu Lab, Hi~, I'm using EAS eQTL data and I don't have ancestry-matched GWAS data. So I want to use TESLA to conduct TWAS analysis, but I'm not sure about the input of the GWAS data. Here are my questions:

  1. Can I use EAS eQTL and a set of Mixed-ancestry GWAS summry data (one summary data including many ancestries) or a set of European ancestry GWAS summary data as input of TESLA?
  2. If could, how should I calculate the MDS information or PCA? I cant only get a AF matrix with 1 rows (GWAS study) and n cols (SNPs).

Thanks Zeno

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Zenoooo commented 9 months ago

Thanks for your reply!