# Apply trained PRS on another dataset

I am using PRSice to compute the PRS over a train set and want to use the coefficient used on the train set to apply it on another set which I will call the test set.

Once I compute the PRS I get a file called analysis.prsice

This is the few first lines

Pheno Set Threshold R2 P Coefficient Standard.Error Num_SNP

- Base 5e-08 0.00550157 0.0659631 -21.0513 11.4492 43

- Base 5.005e-05 0.00396637 0.113759 -61.8545 39.1108 184

- Base 0.00010005 0.00236122 0.220463 -68.9527 56.2742 286

- Base 0.00015005 0.00113035 0.394503 -59.4058 69.7677 382

- Base 0.00020005 0.00072253 0.495129 -55.2605 81.0064 471

- Base 0.00025005 0.000334179 0.642121 -41.5674 89.4432 538

- Base 0.00030005 7.5306e-05 0.825111 -21.391 96.8021 601

- Base 0.00035005 3.95773e-06 0.959527 5.25804 103.612 668

- Base 0.00040005 0.000175506 0.735018 37.723 111.455 743


I thought that I could apply the PRS on another dataset by multiplying the coefficient in the result by the allelic dosage of the corresponding SNPs. However, I am not sure how to know which are the corresponding SNPs of the coefficients.

Also, if there was a command that does that and it would be easier, could you please tell me how to do it?

Thanks

• How does PRSice work, i.e. what ML is it using? What is the accurarcy of your predictions? Applying a trained data set to predict another data set should be straight forward. You don't need to specify individual coefficients
– M__
Oct 17 '20 at 21:06
• I am not sure what you mean? actually, I am not even sure how you measure PRS accuracy. I know in the C+T method that you add the allelic dosage weighted by the effect size in the GWAS Oct 19 '20 at 12:37