Question: Effect Allele Frequency in base summary statistics for PRSs calculation
gravatar for bigfoot
4 days ago by
bigfoot0 wrote:

I want to use summary statistics containing only the Effect Allele Frequency (EAF) and not the Minor Allele Frequency (MAF) as base dataset for PRS calculation in PRSice2. It would be possible to convert EAF to MAF and then filtering for a MAF threshold of 0.01?

Thanks in advance

ADD COMMENTlink modified 3 days ago by Sam2.6k • written 4 days ago by bigfoot0
gravatar for Sam
3 days ago by
New York
Sam2.6k wrote:

If you know the effective allele information, then you can simply filter the effective allele frequency as those > 0.99 and < 0.01. Because if the effective allele frequency is less than 0.01, it's the minor allele.

ADD COMMENTlink modified 1 day ago • written 3 days ago by Sam2.6k

Do you mean 0.49 instead of 0.09?

ADD REPLYlink written 3 days ago by gradstudentNew30

Opps, sorry, should be 0.99. Have now edited

ADD REPLYlink written 1 day ago by Sam2.6k

Thanks Sam. So, in the end, only SNPs with EAF in the range 0.01-0.99 should be retained for the analyses.. right?

ADD REPLYlink written 20 hours ago by bigfoot0
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