How can I calculate PRS for all samples by using PRSice-2.

Question

[MHSATO]

Hi.

I am trying to calculate PRS by using PRSice-2. I'd like to know how to handle the model. When I provide same gwas results to PRSice-2's --base option, is the model always same?

I have several thousands samples measured snp array and target quantitative phenotype. I'd like to calculate PRS for all of these samples. Followings procedures are my plan.

1. GWAS by using randomly selected 3/4 of all samples
2. Construct PRS model by using above result and diagnose of the model by using rest sample.
3. Then, calculate PRS for all samples by using GWAS result used in step 1 and p-threshold in step 2.

For this procedure, I need to confirm that PRSice-2 always construct same model when I use same GWAS result which provided by --base option.

Otherwise, is there another way to fit the model predicted by PRSice-2 to new dataset?

Thanks.