Calculate allele frequencies per population with SNPRelate
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!
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jena •
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irieljoerin •
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irieljoerin •
1 answer
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.
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