Fst from 012 genotype matrix

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9.1 years ago

Jautis ▴ 580

Hi, I'm trying to calculate Fst between populations in R and I am wondering if there is a way to do so from a 012 genotype matrix with missing data (0 being homozygous reference; 2 being homozygous alternate, NA for missing).

I have tried running functions in the R package hierfstat, but get an error message saying there is a non-numeric binary operator.

Any suggestions? Thanks in advance!

Fst Genotype • 2.4k views

ADD COMMENT • link updated 2.2 years ago by Ram 44k • written 9.1 years ago by Jautis ▴ 580

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Hi,

Have you checked that your matrix (or data.frame) is really "numeric"?

And regarding NAs, why not just remove them?

ADD REPLY • link updated 2.2 years ago by Ram 44k • written 9.1 years ago by abascalfederico ★ 1.2k

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Yes, the data frame is actually numeric. It is comprised entirely of 0, 1, 2, and NA. I can't just remove the NAs because every site has at least some individuals called, but none have all individuals called. The NAs occur because this is low coverage sequencing.

ADD REPLY • link updated 2.2 years ago by Ram 44k • written 9.1 years ago by Jautis ▴ 580

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