Polygenic risk score: before or after SNP filtering?
Hi,
I have to calculate the Polygenic Risk Score (PGRS) for a certain phenotype, on two different datasets.
Initially, both datasets contain the same markers, but filtering by MAF/HWE would leave a different subset in each case. I'm thus wondering how to do that filtering (if needed). These are the options:
- Estimating PGRS in each dataset, without any MAF/HWE filtering
- Merging both datasets, filtering by MAF/HWE, and then computing PGRS
- Filtering each dataset by MAF/HWE, re-filtering to leave only SNPs shared across datasets, and then computing PGRS
- Other...
I guess there are some standard guidelines for this, but I haven't found the right references. Any help is appreciated.
Thanks in advance,
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How are you calculating PGRS ? edit: and MAF/HWE for that matter.
Hi,
I'm taking the results from public data (another GWAS), and trying to calculate PGRS in my datasets. My question is basically about how to run QC (MAF/HWE filtering, if any) in the datasets I have.
Thanks
How are you calculating PGRS? How are you calculating HWE? How are you calculating MAF? Are you calculating HWE? Are you calculating MAF? What does PGRS mean?
These questions are important to correctly answer your original question. I'm inclined to say "don't filter by MAF or HWE" but it might be incorrect.
Hi,
Answering your questions:
How are you calculating PGRS? - http://image.slidesharecdn.com/007metspalu-141006151830-conversion-gate01/95/eurobioforum2014speakermetspalu-22-638.jpg?cb=1412608844; I'm using PRSice, by the way
How are you calculating HWE? How are you calculating MAF? Are you calculating HWE? Are you calculating MAF? - With standard plink flags. I'm not sure about whether or not I should calculate them --that's actually the whole point of this post.
Hope this info helps,