I am very new to bioinformatics and come from a quantitative economics background. I was asked to help with a project on creating a risk score consisting of multiple SNPs and since then I have been doing some research on this.
One way to go as I've researched is to do this with a simple math formula, which would be an unweighted approach (like a TGS).
I am interested in the approach of giving weights to the SNPs as this should make the results more accurate(?). My main question is to ask if I understand the process correctly and if my ideas are possible:
I have predetermined SNPs of interest that are associated with a specific trait
calculate/get the betas for the chosen SNPs from GWAS
use these betas to weight and calculate a risk score for my own sample
Is this plausible?
I've read about PLINK and R-packages such as lassosum, PRsice, LDpred and PRS-CS. I don't fully understand the process of what the best way is to calculate/get the betas from GWAS.
I would be really thankful for any tips and help regarding this. Thanks in advance for taking the time to read and respond to my message :)