Calculating Nei's genetic distance and pairwise Fst from HLA allele frequencies

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Mqondisi Mavuso

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Jun 4, 2018, 8:35:04 AM6/4/18

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I have HLA allele frequencies from different populations (attached) and wish to compute Nei's genetic distance and pairwise Fst, any pointers in PoppR if possible

Sincerely

Mqondisi

hlalA allel freq dummy data.csv

Zhian Kamvar

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Jun 6, 2018, 9:57:56 AM6/6/18

to Mqondisi Mavuso, poppr

Hi,

I believe you cannot calculate pairwise Fst with allele frequency data since you don't have any information on heterozygosity.

That being said, you might be able to simulate populations using the rgenotypes function from the mmod package and calculate the statistics on the simulated populations and get confidence intervals. That being said, the function can only simulation one locus and one population at a time, so you will have to construct a couple of loops/lapply functions to get the job done for each of your populations and loci.

Because this question is more general in scope and not specific to poppr, I would recommend posting any questions on the above procedure to the R-SIG-GENETICS mailing list: https://stat.ethz.ch/mailman/listinfo/r-sig-genetics

Hope that helps,

Zhian

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<hlalA allel freq dummy data.csv>