Applying polygenic scores to data
1
1
Entering edit mode
19 months ago
jared ▴ 10

I have a polygenic score file from the PGS catalog and I would like to apply this to my dataset (PLINK format) and calculate risk for my samples. I have some experience using PRSice but I believe the process differs since I have a generate PGS where weights are already calculated for each SNP. What would be the easiest way to do this/is there a tutorial or thread out there (I spent a lot of time, but I can't seem to find anything in my case). The PGS file has columns: rsID, chr_name, chr_position, effect_weight, effect_allele, reference_allele, locus_name.

PGS PRS polygenic SNP PRSice • 798 views
ADD COMMENT
1
Entering edit mode
19 months ago
Sam ★ 3.6k

You can directly use the weight file. PRSice does not modify your weight, so the result will still be valid.

If you are concern about the p-thresholding and clumping, you can simply do --no-clump with --bar-levels 1 --fastscore. This will use all the SNPs to calculate the PRS.

ADD COMMENT
0
Entering edit mode

I would like to calculate the PRS for a bunch of samples in a bgen file. As is the case in this thread, I just have the files from the PGS Catalog. Could you be more specific about how to use PRSice with these files from the PGS catalog ? The problem right now is that PRSice needs P-Values but these are not provided by the pgs catalog. I just have the already calculated weights. Thanks in advance.

ADD REPLY
0
Entering edit mode

you can ask a new question on this.

In short, from the PGS catalog file, add a column called P-value, fill it with a random number between 0 and 1 (doesn't matter what it is). Then you can use --no-clump --fastscore --bar-levels 1 to run PRSice to get the PRS you want.

ADD REPLY

Login before adding your answer.

Traffic: 1303 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6