[adegenet-forum] different results for pegas and hierfstat Fst via weir and cockerham

[Gary Longo]

Hi Thibaut and company!

# I've noticed differences with Fst and Fis calculations in Pegas vs
Hierfstat while using Adegenet

> data("nancycats")

# using weir and cockerham in pegas
> nancycats_Fstat_as_loci <- Fst(as.loci(nancycats))
> nancycats_Fstat_as_loci

            Fit        Fst         Fis
fca8  0.2447420 0.10146648 0.159454807
fca23 0.1646295 0.06746762 0.104191391
fca43 0.1514487 0.06893755 0.088620458
fca45 0.1010807 0.09792456 0.003498722
fca77 0.2790495 0.10036588 0.198618075
fca78 0.1842490 0.07025915 0.122603911
fca90 0.2098744 0.09168833 0.130116240
fca96 0.2034755 0.10744024 0.107595351
fca37 0.2604033 0.06985321 0.204860244

# also using weir & cockerham in hierfstat
> nancycats_hfstat <- genind2hierfstat(nancycats)
> nancycats_wc <- wc(nancycats_hfstat)
> nancycats_wc_loci_stats <- as.data.frame(nancycats_wc[["per.loc"]])
> nancycats_wc_loci_stats

         FST          FIS
1 0.10150515  0.148673460
2 0.06746762  0.104191391
3 0.06893755  0.088620458
4 0.07652596 -0.001451681
5 0.10036588  0.198618075
6 0.07025915  0.122603911
7 0.09168833  0.130116240
8 0.10981110  0.094857474
9 0.06985321  0.204860244


> colSums(is.na(nancycats_hfstat))

  pop  fca8 fca23 fca43 fca45 fca77 fca78 fca90 fca96 fca37
    0    20     0     0    21     0     0     0     9     0


The results are identical in loci that are not missing data but are
different in loci with missing data.

Two questions:
1) How are they handling missing data differently since they are both using
Weir and Cockerham 1984? Follow up: which is better suited for calculating
Fst and Fis values when there are missing data? I'm analyzing a SNP dataset
based on ~2100 RADseq loci in over 500 individuals, which of course has
some missing data at most loci. My results from calculating these values in
Pegas vs Hierfstat are very different. Specifically Fst and Fis values are
generally much higher and I don't get any negative Fis values when
calculated in pegas.

2) Why does the conversion to hierfstat result in the loss of loci name?
This would be very useful to retain for downstream comparisons.

Cheers,
Gary


-- 
Gary Charles Longo
NRC Research Associate
NOAA, National Marine Fisheries Service
2725 Montlake Blvd E
Seattle, WA  98112
garycharleslongo.wordpress.com
(831) 247-3056
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