Entering edit mode
4.7 years ago
bigfoot
▴
10
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
Do you mean 0.49 instead of 0.09?
Opps, sorry, should be 0.99. Have now edited
Thanks Sam. So, in the end, only SNPs with EAF in the range 0.01-0.99 should be retained for the analyses.. right?
If your goal is to filter by MAF of 0.01, then yes.
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?
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