Calculate allele frequencies per population with SNPRelate

Question

[irieljoerin]

Hi all, I am trying to use SNPRelate R package for some analysis and I began calculating allele frequencies from plink data with the function snpgdsSNPRateFreq. However I didn't find any way to do these calculations per group or population. Can anybody help me with that? Or is there any other package apropriate for doing that? Thanks in advance!

Answer 1

[jena]

Hi,

I don't know the SNPRelate package, but you can use plink_to_afs() from the R admixtools2 package. It calculates allele frequency spectra for populations as defined in your plink dataset, but you can also provide your own population definitions.