Hi,
Does anyone know of software that computes Fst values from SNP data encoded as 0, 1, 2, i.e., 0==AA, 1==Aa, 2==aa?
Thanks,
D.
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written
by
Darren J. Fitzpatrick
It looks like the basic.stats function from the hierfstat R package will calculate Fst.
You may need to convert the integers to factors using the factors function. eg:
> data = c(1,2,2,0,1,2,0,0,1,2,0,0,1)
> fdata = factor(data)
> fdata
[1] 1 2 2 0 1 2 0 0 1 2 0 0 1
Levels: 0 1 2
I'm trying to achieve the same and followed your recommendations but it seems like hierfstat only allows 1 and 2 values as input and they are integers not factors in the example given.
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I know that the Pegas package calculates Fst. With some minor file formatting you could use it.
I would also suggest trying to write your own. Fst is pretty easy to implement and worth it.