[adegenet-forum] Per locus pairwise Fst

[Vikram Chhatre]

Thank you for all the replies.  I have been looking at the pp.fst()
function in the Hierfstat package.  Does the post-seploc data frame need to
be converted into something that Hierfstat understands first?  The
following doesn't seem to work:

# Use seploc to separate loci:
gen100_seploc <- seploc(gen100_genind, truenames=TRUE, res.type=c('genind',
'matrix')

# Load Hierfstat
library(hierfstat)

# Calculate pairwise Fst:
gen100_perLocusPWFst <- lapply(gen100_seploc, pp.fst, diploid=TRUE)

Error in unique.default(Pop) : unique() applies only to vectors

On Sat, Sep 13, 2014 at 2:20 PM, Jombart, Thibaut <t.jombart at imperial.ac.uk>
wrote:

>
> Hi there,
>
> yes, this function is not optimized for large datasets. You can use the
> same approach but using functions from the hierfstat package.
>
> Cheers
> Thibaut
> ________________________________________
> From: adegenet-forum-bounces at lists.r-forge.r-project.org [
> adegenet-forum-bounces at lists.r-forge.r-project.org] on behalf of Vikram
> Chhatre [crypticlineage at gmail.com]
> Sent: 12 September 2014 18:31
> To: adegenet-forum at lists.r-forge.r-project.org
> Subject: Re: [adegenet-forum] Per locus pairwise Fst
>
> I am revisiting this topic due to some technical problems.
>
> The task at hand is to estimate pairwise Fst matrices for each locus
> separately.
>
> # Genind object is stored in:
> gen100_genind
>
> # Use seploc to separate loci:
> gen100_seploc <- seploc(gen100_genind, truenames=TRUE,
> res.type=c('genind', 'matrix')
>
> # Calculate pairwise Fst:
> gen100_perLocusPWFst <- lapply(gen100_seploc, pairwise.fst,
> res.type=c('dist', 'matrix'), trunames=TRUE)
>
> For a data set consisting of 30 populations, 20 individuals each, 1000
> loci and 2 alleles per locus (1.2 million data points), it takes up to 6
> hours to estimate the pairwise Fst matrix with this method.
>
> Is there any way to speed this up?  Should I look into any other packages?
>
> Many thanks for your time and help.
> Vikram
>
>
>
>
> On Mon, Jul 14, 2014 at 9:16 AM, Vikram Chhatre <crypticlineage at gmail.com
> <mailto:crypticlineage at gmail.com>> wrote:
> Perfect!  Thank you for both solutions.
>
> V
>
>
> On Mon, Jul 14, 2014 at 9:13 AM, Jombart, Thibaut <
> t.jombart at imperial.ac.uk<mailto:t.jombart at imperial.ac.uk>> wrote:
>
> Hi there,
>
> you can use seploc to separate loci, and lapply over the resulting list
> using your prefered fst function.
>
> Cheers
> Thibaut
> ________________________________________
> From: adegenet-forum-bounces at lists.r-forge.r-project.org<mailto:
> adegenet-forum-bounces at lists.r-forge.r-project.org> [
> adegenet-forum-bounces at lists.r-forge.r-project.org<mailto:
> adegenet-forum-bounces at lists.r-forge.r-project.org>] on behalf of Vikram
> Chhatre [crypticlineage at gmail.com<mailto:crypticlineage at gmail.com>]
> Sent: 14 July 2014 14:01
> To: adegenet-forum at lists.r-forge.r-project.org<mailto:
> adegenet-forum at lists.r-forge.r-project.org>
> Subject: [adegenet-forum] Per locus pairwise Fst
>
> Good morning.
>
> I would like to estimate per locus pairwise Fst for populations, but it
> appears that Adegenet only estimates this over all loci (i.e. single
> matrix).  What I would like is one matrix per locus.  Has anyone modified
> the functions or know of alternative programs that can do this?
>
> Thanks
> Vikram
>
>
>
>
>
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