Question: Effect Allele Frequency in base summary statistics for PRSs calculation
1
gravatar for bigfoot
9 months ago by
bigfoot10
bigfoot10 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 9 months ago by Sam3.3k • written 9 months ago by bigfoot10
1
gravatar for Sam
9 months ago by
Sam3.3k
New York
Sam3.3k 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 9 months ago • written 9 months ago by Sam3.3k

Do you mean 0.49 instead of 0.09?

ADD REPLYlink written 9 months ago by gradstudentNew30

Opps, sorry, should be 0.99. Have now edited

ADD REPLYlink written 9 months ago by Sam3.3k

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 9 months ago by bigfoot10

If your goal is to filter by MAF of 0.01, then yes.

ADD REPLYlink written 9 months ago by Sam3.3k

As a follow-up, what if our summary statistics only contain the alternative allele frequency and we would like to filter on a MAF threshold? Could we go through the same process of do we first need to transform the alternative allele frequency somehow?

ADD REPLYlink written 11 weeks ago by rem0

You can change the alternative allele frequency to MAF by making sure the frequency is less than 0.5. So for any frequency > 0.5, do 1- frequency and you'll have the MAF

ADD REPLYlink written 11 weeks ago by Sam3.3k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1098 users visited in the last hour