dajiangliu / raregwama Goto Github PK

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

Dear Liu Lab,

I want to use TESLA to run multi-ancestry TWAS analysis, but the wiki and help doc make me confused. Since our GWAS summary statistics were not generated by rvtest, some variables, such as HWE, Call_rate, etc., were not included in our results. I wonder to know which variables are necessary.

Thanks
tql

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

I'm trying to do a conditional analysis using rvtests generated input files. In some studies for a given chromosome and position, the REF/ALT might be C/T while others may have it coded oppositely as REF/ALT T/C. It seems that rareGWAMA treats these as two different variants rather than being equivalent (whereas RAREMETAL and METAL handle the flipping internally). Is there any way of having rareGWAMA handle this internally rather than having to reformat the summary statistics files?