[adegenet-forum] Fst(as.loci(pinus.genind)) return NaN for all F statistics

[Thibaut Jombart]

Hi there,

it is a bit hard to figure things out as we don't see the outputs of
several commands and there is no reproducible example, but your import of
the data looks good to me. It could be too many missing data in one of your
groups, or a fixed locus?

Maybe worth checking allele counts per populations:
tab(genind2genpop(pinus.genind))

Best
Thibaut


--
Dr Thibaut Jombart
Lecturer, Department of Infectious Disease Epidemiology, Imperial College
London
Head of RECON: repidemicsconsortium.org
WHO Consultant - outbreak analysis
https://thibautjombart.netlify.com
Twitter: @TeebzR
+44(0)20 7594 3658

On 24 June 2018 at 02:31, Marcelo Laia <marcelolaia at gmail.com> wrote:

> Dear all,
>
> I try to use adegenet for the first time.
>
> library("ape")
> library("pegas")
> library("seqinr")
> library("ggplot2")
> library("adegenet")
>
> pinus.data <- read.table("Analises_pinus_individual.csv", header=TRUE,
>                          sep="\t", row.names = 1)
> head(pinus.data)
> > head(pinus.data)
>    PTTX3081 RIPT0031 PTTX3011 PTTX2037 PTTX311 Populacao
> 1    186243   235284   131155   190190  191191    POP001
> 3    177235   235235   131155   190190  191195    POP003
> 15   177239   235235   131155   190190  191191    POP015
> 16   177254   235235   131155   190190  191195    POP016
> 17   177235   235235       NA   190190  191195    POP017
> 19   177235   235235   131155   190190  191195    POP019
> >
>
> pinus.genind <- df2genind(pinus.data[, 1:5], ploidy=2, ncode=3, NA.char =
> "NA",
>                           pop = pinus.data$Populacao, type = "codom")
> pinus.genind
> tab(pinus.genind)
> popNames(pinus.genind)
> indNames(pinus.genind)
> locNames(pinus.genind)
>
> > is.genind(pinus.genind)
> [1] TRUE
> >
>
> > Fst(as.loci(pinus.genind))
>          Fit Fst Fis
> PTTX3081 NaN NaN NaN
> RIPT0031 NaN NaN NaN
> PTTX3011 NaN NaN NaN
> PTTX2037 NaN NaN NaN
> PTTX311  NaN NaN NaN
>
> The col "Populacao" in file Analises_pinus_individual.csv is the pop slot.
> I
> consider each individual from a different population.
>
> Please, could you help me?
>
> Thank you very much!
>
> --
> Laia, ML
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