Hi,
I am new to Bioinformatics and I would really appreciate some help with my new project. I am trying to calculate and interpret Polygenic Risk Score that I got with Model 4 described in this paper (page 9):
In Table 3 - Supplementary Data (at the end of the page) there is a list of all SNPs used in the model with the corresponding weights (betas). To observe the PRS distribution on a test set, I did the following:
I used R package: MafDb.gnomAD.r2.0.1.GRCh38 to get a MAF for each SNP listed in Sup. Table 3. Then I calculated the expected genotype frequencies under random mating using Hardy–Weinberg principle and used these frequencies to generate genotype data; more specifically, I generated the number of reference alleles for each pair (SNP, sample) which is either 0, 1 or 2 (g_it from the model mentioned above).
I plotted the distribution of PRS values and I got this:
Now I am a bit confused about how to interpret these results. I would like to get the interpretation in the form of relative risk. Any tips on how to do that are welcome.
Thanks! :)
