[adegenet-forum] pairwise.fst in the basic tutorial

[Tyler Smith]

Thanks!


Amaranta writes:

> Dear Tyler,
>
> Only some functions in hierfstat work with genind objects, but all of them
> work with hierfstat objects, which you can obtain with
>
> genind2hierfstat(dat,pop=NULL)
>
> There is a number of functions in hierfstat calculating pairwise Fst,
> with different methods
> genet.dist <http://127.0.0.1:16265/help/library/hierfstat/html/genet.dist.html>
> () offers a range of fst methods
>
> betas() calculates a newer measure of FST (WG 2017), $betaW is the
> average FST across  pops, so if you feed it with a dataset of 2
> populations, it will give like a pairwise FST.
>
> and fst.dosage() also calculates pairwise population WG17 for SNP
> data, but has some issues with NA at the moment.
>
> Hope is helpful,
>
> All the best,
>
> ----------------------------------------------------------
> Amaranta Fontcuberta, graduate assistant
> Dept. Écologie et Évolution
> Université de Lausanne
>
>
> Missatge de Tyler Smith <tyler at plantarum.ca> del dia dc., 25 de març 2020 a
> les 17:17:
>
>> Hello,
>>
>> The basic tutorial includes instructions to use the function
>> `pairwise.fst`, which I believe was once part of the package
>> `hierfstat`. That function no longer exists, and the closest match in
>> `hierfstat` is `pairwise.neifst`. That function won't work on a `genind`
>> object:
>>
>>
>> ```
>> > data(nancycats)
>> > pairwise.fst(nancycats)
>> Error in pairwise.fst(nancycats) : could not find function "pairwise.fst"
>> > pairwise.neifst(nancycats)
>> Error in names(y) <- nm[!nas] :
>>   'names' attribute [11] must be the same length as the vector [1]
>> In addition: Warning message:
>> In is.na(x) : is.na() applied to non-(list or vector) of type 'S4'
>> ```
>>
>> Is there a way to calculate pairwise Fst for genind objects now?
>>
>> Thanks,
>>
>> Tyler
>>
>> --
>> Tyler Smith
>> http://plantarum.ca
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-- 
Tyler Smith
http://plantarum.ca