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

[Marcelo Laia]

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